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z{5soVM3oj7ex_tVF9F3XK_W#NWBw^1JvWZ`b{lVV4*?I-kcVd+_c&1{qMmPGnWBXy j`0hU&07zOF%BD~Syq Date: Thu, 18 Jul 2024 18:03:01 -0400 Subject: [PATCH 02/40] Add logo to README --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 6c8559342..4f276eb95 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,7 @@ # OntoGPT +![OntoGPT Logo](/images/ontogpt_logo_3.jpg) + [![DOI](https://zenodo.org/badge/13996/monarch-initiative/ontogpt.svg)](https://zenodo.org/badge/latestdoi/13996/monarch-initiative/ontogpt) ![PyPI](https://img.shields.io/pypi/v/ontogpt) From fcddb3a1b7937d7b8aac3d3cc97be0e974e28dc4 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Thu, 18 Jul 2024 18:05:16 -0400 Subject: [PATCH 03/40] Remove misplaced outputs --- disease_cp_output.yaml | 612 --------- long_output.yaml | 2873 ---------------------------------------- txt_cases_results.tsv | 1331 ------------------- 3 files changed, 4816 deletions(-) delete mode 100644 disease_cp_output.yaml delete mode 100644 long_output.yaml delete mode 100644 txt_cases_results.tsv diff --git a/disease_cp_output.yaml b/disease_cp_output.yaml deleted file mode 100644 index 5a68599fe..000000000 --- a/disease_cp_output.yaml +++ /dev/null @@ -1,612 +0,0 @@ -input_text: |- - Title: Symptoms of anxiety and depression associated with steroid efficacy and clinical outcomes in patients with inflammatory bowel disease. - Keywords: HADS; anxiety; depression; inflammatory bowel disease; steroid resistance - PMID: 37547213 - Abstract: Anxiety and depression symptoms are very common in patients with inflammatory bowel disease (IBD). We aimed to explore the impact of anxiety and depression on the efficacy of medications, as well as IBD-related poor outcomes.This was a prospective longitudinal observational study. Hospital Anxiety and Depression Scale was used to assess anxiety and depression symptoms. Logistic regression analyses were used to assess the association between anxiety/depression and the response to different medications. Kaplan-Meier survival analysis and Cox regression model were applied to analyze the relationship between anxiety/depression and IBD-related poor outcomes, which were defined as urgent IBD-related hospitalization, IBD-related surgery, or death.A total of 325 IBD patients were enrolled, 118 of whom were treated with corticosteroids, 88 with azathioprine/6-mercaptopurine (AZA/6-MP), and 147 with anti-TNF agents. Anxiety/depression symptoms were found to be significantly related to steroid resistance, but independent of AZA/6-MP and anti-TNF agents nonresponse. There was a significant association between anxiety/depression symptoms and IBD-related poor outcomes. Coexisting with anxiety/depression symptoms was an independent influencing factor of steroid resistance and IBD-related poor outcomes.IBD patients with anxiety/depression symptoms were at a higher risk of developing steroid resistance and IBD-related poor outcomes. Future studies are needed to explore whether interventions for anxiety and depression will improve their response to medications and change their prognosis.Copyright © 2023 Duan, Yang, Cao, Chen, Liang and Zhang. -raw_completion_output: |- - genes: N/A - exposures: corticosteroids, azathioprine/6-mercaptopurine (AZA/6-MP), anti-TNF agents - gene_exposures_relationships: N/A - diseases: inflammatory bowel disease - cellular_process: N/A - disease_cellular_process_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - corticosteroids, azathioprine/6-mercaptopurine (AZA/6-MP), anti-TNF agents - gene_exposures_relationships: - - subject: N/A - predicate: N/A - object: N/A - qualifier: N/A - subject_qualifier: N/A - object_qualifier: N/A - diseases: - - MONDO:0005265 - cellular_process: - - N/A - disease_cellular_process_relationships: - - subject: N/A - predicate: N/A - object: N/A - qualifier: N/A - subject_qualifier: N/A - object_qualifier: N/A -named_entities: - - id: MONDO:0005265 - label: inflammatory bowel disease -input_text: |- - Title: Hypoxia-sensing by the Histone Demethylase UTX ( KDM6A ) Controls Colitogenic CD4 + T cell Fate and Mucosal Inflammation. - Keywords: - PMID: 37546969 - Abstract: Hypoxia is a feature of inflammatory conditions [e.g., inflammatory bowel disease (IBD)] and can exacerbate tissue damage in these diseases. To counteract hypoxia's deleterious effects, adaptive responses have evolved which protect against hypoxia-associated tissue injury. To date, much attention has focused on hypoxia-activated HIF (hypoxia-inducible factor) transcription factors in these responses. However, recent work has identified epigenetic regulators that are also oxygen-sensitive, but their role in adaptation to hypoxic inflammation is currently unclear. Here, we show that the oxygen-sensing epigenetic regulator UTX is a critical modulator of colitis severity. Unlike HIF transcription factors that act on gut epithelial cells, UTX functions in colitis through its effects on immune cells. Hypoxia results in decreased CD4 + T cell IFN-γ production and increased CD4 + regulatory T cells, and these findings are recapitulated by T cell-specific UTX deficiency. Hypoxia impairs the histone demethylase activity of UTX, and loss of UTX function leads to accumulation of repressive H3K27me3 epigenetic marks at IL12/STAT4 pathway genes ( Il12rb2, Tbx21, and Ifng ). In a colitis mouse model, T cell-specific UTX deletion ameliorates colonic inflammation, protects against weight loss, and increases survival. Together these findings implicate UTX's oxygen-sensitive histone demethylase activity in mediating protective, hypoxia-induced pathways in colitis. -raw_completion_output: |- - genes: UTX, HIF, IL12rb2, Tbx21, Ifng - exposures: hypoxia - gene_exposures_relationships: UTX - hypoxia - diseases: inflammatory bowel disease (IBD), colitis - cellular_process: CD4 + T cell IFN-γ production, CD4 + regulatory T cells - disease_cellular_process_relationships: colitis - CD4 + T cell IFN-γ production, CD4 + regulatory T cells -prompt: |+ - From the text below, extract the following entities in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - colitis - CD4 + T cell IFN-γ production, CD4 + regulatory T cells - - === - -extracted_object: - genes: - - UTX, HIF, IL12rb2, Tbx21, Ifng - exposures: - - hypoxia - gene_exposures_relationships: - - subject: UTX - predicate: hypoxia - object: None - qualifier: None - subject_qualifier: None - object_qualifier: None - diseases: - - MONDO:0005052 - cellular_process: - - CD4 + T cell IFN-γ production, CD4 + regulatory T cells - disease_cellular_process_relationships: - - subject: MONDO:0005292 - predicate: regulatory - object: CD4 + T cells - subject_qualifier: None - object_qualifier: None -named_entities: - - id: MONDO:0005052 - label: inflammatory bowel disease (IBD), colitis - - id: MONDO:0005292 - label: colitis -input_text: |- - Title: Iranian Consensus Guideline for Pharmacotherapy with Biologics and Small Molecules Drugs in Adults with Inflammatory Bowel Diseases. - Keywords: Biologic drugs; Consensus guideline; Pharmacotherapy; Small therapeutic molecules - PMID: 37546508 - Abstract: Background: Pharmacotherapy with biologics and small molecules, as the more effective therapies for moderate to severe ulcerative colitis (UC) and Crohn's disease (CD), is complex. Choosing the best methods for their utilization in order to induce and maintain remission are critical for practicing gastroenterologists. We aimed to develop an Iranian consensus on the management of inflammatory bowel disease (IBD) patients with biologics and small molecules. Methods: A Delphi consensus was undertaken by experts who performed a literature summary and voting process. Quality of evidence was assessed using the Grading and Recommendations Assessment, Development, and Evaluation; and an additional risk of bias-protocol. Results: Following an extensive search of the literature, 219 studies were used to determine the quality of the evidence. After three rounds of voting, consensus (defined as≥80% agreement) was reached for 87 statements. Conclusion: We considered different aspects of pharmacotherapy in this consensus. This guideline, along with clinical judgment, can be used to optimize management of IBD patients.© 2023 Middle East Journal of Digestive Diseases. -raw_completion_output: |- - genes: None mentioned in the text - exposures: Biologic drugs; Small therapeutic molecules - gene_exposures_relationships: None mentioned in the text - diseases: Inflammatory bowel disease (IBD); Ulcerative colitis (UC); Crohn's disease (CD) - cellular_process: None mentioned in the text - disease_cellular_process_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - Biologic drugs - - Small therapeutic molecules - gene_exposures_relationships: - - subject: None mentioned in the text - predicate: None mentioned in the text - object: None mentioned in the text - qualifier: None mentioned in the text - subject_qualifier: None mentioned in the text - object_qualifier: None mentioned in the text - diseases: - - MONDO:0005052 - - MONDO:0005101 - - MONDO:0016063 - cellular_process: - - None mentioned in the text - disease_cellular_process_relationships: - - subject: None mentioned in the text - predicate: None mentioned in the text - object: None mentioned in the text - qualifier: None mentioned in the text - subject_qualifier: None mentioned in the text - object_qualifier: None mentioned in the text -named_entities: - - id: MONDO:0005052 - label: Inflammatory bowel disease (IBD) - - id: MONDO:0005101 - label: Ulcerative colitis (UC) - - id: MONDO:0016063 - label: Crohn's disease (CD) -input_text: |- - Title: Whipple's Disease; An Overlooked Diagnosis. - Keywords: COVID-19; Malabsorption syndrome; Whipple disease - PMID: 37546505 - Abstract: Whipple disease is a rare multisystem inflammatory disease. Because fewer than 1000 reported cases have been described, clinical experience with this disorder is sparse. We are reporting a case of a 46-year-old man who presented with fever, weight loss, and polyarthralgia for 2 months, and 1 month of diarrhea. The patient was thoroughly investigated for collagen diseases and COVID-19, with no definite diagnosis. A therapeutic trial by immunosuppressive drugs provided partial remission followed by a marked rebound of the symptoms. His occult blood in stool was positive and subsequent upper endoscopy with proximal small intestinal biopsies showed the pathological features of Whipple's disease. The patient showed a dramatic improvement following treatment with ceftriaxone and trimethoprim-sulfamethoxazole. Despite the rarity of Whipple's disease, its course mimics many rheumatological diseases, inflammatory bowel disease, and COVID-19 disease. It should always be a part of the differential diagnosis of obscure polyarthralgia and chronic diarrhea.© 2023 Middle East Journal of Digestive Diseases. -raw_completion_output: |- - genes: not mentioned in the text - exposures: not mentioned in the text - gene_exposures_relationships: not mentioned in the text - diseases: Whipple's disease; COVID-19; Malabsorption syndrome - cellular_process: not mentioned in the text - disease_cellular_process_relationships: not mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - not mentioned in the text - - === - -extracted_object: - genes: - - not mentioned in the text - exposures: - - not mentioned in the text - gene_exposures_relationships: - - subject: not mentioned in the text - predicate: not mentioned in the text - object: not mentioned in the text - qualifier: not mentioned in the text - subject_qualifier: not mentioned in the text - object_qualifier: not mentioned in the text - diseases: - - MONDO:0005116 - - MONDO:0100096 - - MONDO:0020598 - cellular_process: - - not mentioned in the text - disease_cellular_process_relationships: - - subject: not mentioned - predicate: not mentioned - object: not mentioned - qualifier: not mentioned - subject_qualifier: not mentioned - object_qualifier: not mentioned -named_entities: - - id: MONDO:0005116 - label: Whipple's disease - - id: MONDO:0100096 - label: COVID-19 - - id: MONDO:0020598 - label: Malabsorption syndrome -input_text: |- - Title: Bowel-associated dermatosis-arthritis syndrome (BADAS): a narrative review. - Keywords: bacterial translocation; bariatric surgery; bowel-associated dermatosis-arthritis syndrome; inflammatory bowel disease; neutrophilic dermatosis - PMID: 37545820 - Abstract: Bowel-associated dermatosis-arthritis syndrome is a neutrophilic dermatosis presenting with flu-like symptoms, arthritis and skin lesions. The type of skin presentation varies although typically consists of red patches progressing into papulopustular-type lesions. Initially, the pathogenesis of the disease was linked exclusively to bariatric surgery, but more recent reports indicate the role of gastrointestinal diseases resulting in bacterial overgrowth and consequent translocation of bacteria into the bloodstream. The disease may resolve spontaneously, however sometimes requires a treatment aimed at managing inflammation and excessive bacterial overgrowth, and therefore antibiotic therapy, immunosuppressive drugs, biological treatment and sometimes intestinal surgeries are applied.Copyright: © 2023 Termedia Sp. z o. o. -raw_completion_output: |- - genes: Not mentioned in the text - exposures: bacterial translocation; bariatric surgery; inflammatory bowel disease; gastrointestinal diseases; bacterial overgrowth - gene_exposures_relationships: Not mentioned in the text - diseases: Bowel-associated dermatosis-arthritis syndrome; neutrophilic dermatosis - cellular_process: Not mentioned in the text - disease_cellular_process_relationships: Not mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - Not mentioned in the text - - === - -extracted_object: - genes: - - Not mentioned in the text - exposures: - - bacterial translocation - - bariatric surgery - - inflammatory bowel disease - - gastrointestinal diseases - - bacterial overgrowth - gene_exposures_relationships: - - subject: Not mentioned in the text - predicate: Not mentioned in the text - object: Not mentioned in the text - qualifier: Not mentioned in the text - subject_qualifier: Not mentioned in the text - object_qualifier: Not mentioned in the text - diseases: - - Bowel-associated dermatosis-arthritis syndrome - - neutrophilic dermatosis - cellular_process: - - Not mentioned in the text -input_text: |- - Title: Stigma and its correlates among patients with Crohn's disease: A cross-sectional study in China. - Keywords: China; Crohn’s disease; Self-efficacy; Social support; Stigma - PMID: 37545781 - Abstract: Crohn's disease is an incurable disease characterized by unpredictable intestinal symptoms, which unavoidably affect patients' lives and contribute to feelings of stigma. This study aimed to explore the status and its correlates of stigma among patients with Crohn's disease.Using a convenience sampling, 146 hospitalized patients with Crohn's disease were recruited in a tertiary hospital in Southern China from October 2020 to March 2021. The participants were assessed by demographic and disease-related questionnaires, the Social Impact Scale (SIS), Inflammatory Bowel Disease-Self-Efficacy Scale (IBD-SES), and Social Support Rating Scale (SSRS). Multivariate linear regression analysis was conducted to explore the influencing factors of stigma among patients with Crohn's disease.The mean SIS score was 58.14 ± 10.74, representing a moderate effect of stigma, and 85.6% (125/146) of the patients experienced moderate to high levels of stigma. The multiple linear regression analysis showed that perceived public awareness of the disease, family income, age, and self-efficacy were the main influencing factors of stigma, which could explain 52% of the total variation of stigma among patients with Crohn's disease.Stigma among patients with Crohn's disease is influenced by perceived public awareness of the disease, family income, age, and self-efficacy. Interventions aimed at improving self-efficacy and public awareness should be considered to alleviate the level of stigma, especially for those aged 40 years or older or low-income patients.© 2023 The Authors. -raw_completion_output: |- - genes: No genes mentioned in the text. - exposures: No exposures mentioned in the text. - gene_exposures_relationships: No gene-exposure relationships mentioned in the text. - diseases: Crohn's disease - cellular_process: No cellular processes mentioned in the text. - disease_cellular_process_relationships: No disease-cellular process relationships mentioned in the text. -prompt: |+ - From the text below, extract the following entities in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - No disease-cellular process relationships mentioned in the text. - - === - -extracted_object: - genes: - - No genes mentioned in the text. - exposures: - - No exposures mentioned in the text. - gene_exposures_relationships: - - subject: No gene-exposure relationships mentioned in the text. - predicate: None - object: None - qualifier: None - subject_qualifier: None - object_qualifier: None - diseases: - - MONDO:0005011 - cellular_process: - - No cellular processes mentioned in the text. - disease_cellular_process_relationships: - - subject: None - predicate: None - object: None - qualifier: None - subject_qualifier: None - object_qualifier: None -named_entities: - - id: MONDO:0005011 - label: Crohn's disease -input_text: |- - Title: Bile acids and their receptors: Potential therapeutic targets in inflammatory bowel disease. - Keywords: Bile acid metabolism; Bile acid receptors; Bile acids; Gut microbiota; Inflammatory bowel disease; Intestinal immunology - PMID: 37545642 - Abstract: Chronic and recurrent inflammatory disorders of the gastrointestinal tract caused by a complex interplay between genetics and intestinal dysbiosis are called inflammatory bowel disease. As a result of the interaction between the liver and the gut microbiota, bile acids are an atypical class of steroids produced in mammals and traditionally known for their function in food absorption. With the development of genomics and metabolomics, more and more data suggest that the pathophysiological mechanisms of inflammatory bowel disease are regulated by bile acids and their receptors. Bile acids operate as signalling molecules by activating a variety of bile acid receptors that impact intestinal flora, epithelial barrier function, and intestinal immunology. Inflammatory bowel disease can be treated in new ways by using these potential molecules. This paper mainly discusses the increasing function of bile acids and their receptors in inflammatory bowel disease and their prospective therapeutic applications. In addition, we explore bile acid metabolism and the interaction of bile acids and the gut microbiota.©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved. -raw_completion_output: |- - genes: N/A - exposures: bile acids; gut microbiota - gene_exposures_relationships: N/A - diseases: inflammatory bowel disease - cellular_process: bile acid metabolism; epithelial barrier function; intestinal immunology - disease_cellular_process_relationships: inflammatory bowel disease to bile acid metabolism; inflammatory bowel disease to epithelial barrier function; inflammatory bowel disease to intestinal immunology -prompt: |+ - Split the following piece of text into fields in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - inflammatory bowel disease to intestinal immunology - - === - -extracted_object: - genes: - - N/A - exposures: - - CHEBI:3098 - - gut microbiota - gene_exposures_relationships: - - subject: N/A - predicate: N/A - object: N/A - qualifier: N/A - subject_qualifier: N/A - object_qualifier: N/A - diseases: - - MONDO:0005265 - cellular_process: - - GO:0008206 - - epithelial barrier function - - intestinal immunology - disease_cellular_process_relationships: - - subject: MONDO:0005265 - predicate: to - object: GO:0008206 - - subject: MONDO:0005265 - predicate: to - object: epithelial barrier function - qualifier: N/A - subject_qualifier: N/A - object_qualifier: N/A - - subject: MONDO:0005265 - predicate: to - object: intestinal immunology -named_entities: - - id: CHEBI:3098 - label: bile acids - - id: MONDO:0005265 - label: inflammatory bowel disease - - id: GO:0008206 - label: bile acid metabolism -input_text: |- - Title: Azathioprine monotherapy withdrawal in inflammatory bowel diseases: A retrospective mono-centric study. - Keywords: Azathioprine; Crohn's Disease; Inflammatory bowel diseases; Relapse; Side effects; Ulcerative Colitis - PMID: 37545640 - Abstract: There is no consensus on the recommended duration of and optimal time to stop azathioprine (AZA) therapy in inflammatory bowel disease (IBD). Determining the optimal duration and cessation time can help to balance the risks of long-term intake with the possibility of relapse after cessation.To describe the events following AZA cessation.Retrospective analysis was performed to examine data from adult patients affected by IBD who were followed at the University of Padua and had started but then discontinued AZA between 1995 and 2022. Data on therapy duration, reasons for cessation, and type of relapse after cessation were collected. Cox regression models were used to estimate the risk of relapse in different subgroups.A total of 133 ulcerative colitis patients and 141 Crohn's disease patients were included. Therapy with AZA was stopped in the 1st year in approximately 34% of patients but was continued for more than 10 years in approximately 10% of cases. AZA discontinuation was due to primary failure or disease relapse in 30% of patients and due to disease remission in 25.2% of patients. Most of the remaining cases stopped AZA therapy due to side effects (primarily clinical intolerance, cytopenia, and pancreatic disease). Patients who stopped AZA for clinical remission had an 83% lower risk of relapse during the observation time than other groups, with a relapse-free rate of 89% after 1 year and 79% after 2 years.AZA administration is effective and safe, but it requires careful monitoring for potential minor and major side effects. Only 10% of patients who achieved remission with AZA needed a new treatment within 1 year of drug interruption.©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved. -raw_completion_output: |- - genes: N/A - exposures: Azathioprine - gene_exposures_relationships: N/A - diseases: Crohn's Disease, Inflammatory bowel diseases, Ulcerative Colitis - cellular_process: N/A - disease_cellular_process_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - CHEBI:2948 - gene_exposures_relationships: - - subject: N/A - predicate: N/A - object: N/A - qualifier: N/A - subject_qualifier: N/A - object_qualifier: N/A - diseases: - - Crohn's Disease, Inflammatory bowel diseases, Ulcerative Colitis - cellular_process: - - N/A - disease_cellular_process_relationships: - - subject: N/A - predicate: N/A - object: N/A - qualifier: N/A - subject_qualifier: N/A - object_qualifier: N/A -named_entities: - - id: CHEBI:2948 - label: Azathioprine -input_text: |- - Title: Niacin modulates depressive-like behavior in experimental colitis through GPR109A-dependent mechanisms. - Keywords: BBB; DSS; Depression; GPR109A; Niacin; Sirt1 - PMID: 37544378 - Abstract: Depression is one of the common neurological comorbidities in patients with inflammatory bowel disease (IBD). The current study aimed to investigate the potential impact of niacin on colitis-induced depressive-like behavior in rats.Animals were given 5 % dextran sulfate sodium (DSS) in drinking water for one week to induce colitis. Niacin (80 mg/kg), with or without mepenzolate bromide (GPR109A blocker), was administered once per day throughout the experimental period. Rats were tested for behavioral changes using open field and forced swimming tests.Niacin significantly ameliorated DSS-induced behavioral deficits and alleviated macroscopic and microscopic colonic inflammatory changes. It also augmented the hippocampal levels of ZO-1, occludin, and claudin-5 proteins, indicating the ability of niacin to restore the blood-brain barrier (BBB) integrity. Moreover, niacin decreased hippocampal IL-1ꞵ and NF-ĸB contents but increased GSH, Sirt-1, Nrf-2, HO-1 concentrations. All these beneficial effects were partially abolished by the co-administration of mepenzolate bromide.The neuroprotective effect of niacin against DSS-induced depressive-like behavior was partially mediated through GPR109A-mediated mechanisms. Such mechanisms are also involved in modulating neuronal oxidative stress and inflammation via Sirt-1/Nrf-2/HO-1 signaling pathways.Copyright © 2023. Published by Elsevier Inc. -raw_completion_output: |- - genes: Sirt1, Nrf-2, HO-1, IL-1ꞵ, NF-ĸB - exposures: niacin, mepenzolate bromide, dextran sulfate sodium (DSS) - gene_exposures_relationships: niacin-GPR109A; mepenzolate bromide-GPR109A; DSS-colitis - diseases: depression, inflammatory bowel disease (IBD) - cellular_process: blood-brain barrier (BBB) integrity, oxidative stress, inflammation - disease_cellular_process_relationships: depression-BBB integrity, depression-oxidative stress, depression-inflammation, IBD-BBB integrity, IBD-oxidative stress, IBD-inflammation -prompt: |+ - From the text below, extract the following entities in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - depression-BBB integrity, depression-oxidative stress, depression-inflammation, IBD-BBB integrity, IBD-oxidative stress, IBD-inflammation - - === - -extracted_object: - genes: - - Sirt1, Nrf-2, HO-1, IL-1ꞵ, NF-ĸB - exposures: - - CHEBI:191875 - gene_exposures_relationships: - - subject: niacin-GPR109A - object: HGNC:24827 - subject_qualifier: niacin - - subject: CHEBI:6753 - predicate: '-' - object: HGNC:24827 - qualifier: '-' - subject_qualifier: '-' - object_qualifier: '-' - - subject: DSS-colitis - diseases: - - MONDO:0005052 - cellular_process: - - blood-brain barrier (BBB) integrity, oxidative stress, inflammation - disease_cellular_process_relationships: - - subject: MONDO:0005052 - predicate: inflammation -named_entities: - - id: CHEBI:191875 - label: niacin, mepenzolate bromide, dextran sulfate sodium (DSS) - - id: HGNC:24827 - label: GPR109A - - id: CHEBI:6753 - label: mepenzolate bromide - - id: MONDO:0005052 - label: depression, inflammatory bowel disease (IBD) -input_text: |- - Title: Body Composition in Inflammatory Bowel Disease. - Keywords: Body composition; Clinical outcomes; Inflammatory bowel disease; Treatment strategies - PMID: 37543940 - Abstract: Inflammatory bowel disease (IBD) is associated with body composition changes, which are associated with clinical prognosis, response to therapy, and quality of life in IBD patients. Therefore, it is critical to review the body composition distribution in IBD, summarize the potential factors affecting body composition distribution, and take steps to improve the body composition distribution of IBD patients as early as possible. In the current review, we searched PubMed via keywords 'inflammatory bowel disease', or 'IBD', or 'Crohn's disease', or 'CD', or 'ulcerative colitis', or 'UC', and 'body composition'. Malnutrition and sarcopenia are common in IBD patients and are associated with the clinical course, prognosis, and need for surgery. Disease activity, reduced nutrition intake, vitamin D deficiency, and intestinal dysbiosis are factors contributing to changed body composition. Early use of biological agents to induce remission is critical to improving body composition distribution in IBD patients, supplementation of vitamin D is also important, and moderate physical activity is recommended in IBD patients with clinical remission.© 2023 The Author(s). This is an open-access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. -raw_completion_output: |- - genes: Not mentioned in the text - exposures: vitamin D deficiency, intestinal dysbiosis - gene_exposures_relationships: Not mentioned in the text - diseases: Inflammatory bowel disease, Crohn's disease, ulcerative colitis - cellular_process: Not mentioned in the text - disease_cellular_process_relationships: Not mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - Not mentioned in the text - - === - -extracted_object: - genes: - - Not mentioned in the text - exposures: - - vitamin D deficiency, intestinal dysbiosis - gene_exposures_relationships: - - subject: Not mentioned in the text - predicate: Not mentioned in the text - object: Not mentioned in the text - qualifier: Not mentioned in the text - subject_qualifier: Not mentioned in the text - object_qualifier: Not mentioned in the text - diseases: - - Inflammatory bowel disease, Crohn's disease, ulcerative colitis - cellular_process: - - Not mentioned in the text -input_text: |- - Title: Economic Burden of Inflammatory Bowel Disease in Shiraz, Iran. - Keywords: Direct costs; Economic burden; Indirect costs; Inflammatory bowel diseases - PMID: 37543918 - Abstract: The epidemiological burden of chronic diseases and their risk factors is increasing all over the world, especially in developing and low-income countries. Inflammatory bowel disease (IBD) is one of the chronic diseases which has imposed a great financial burden on individuals and the society.The current study aimed at estimating the economic burden of IBD among 90 patients with IBD who referred to Namazi hospital and Motahari clinic of Shiraz in 2019. The costs to patients were monitored for a year to detect their expenses.This study is descriptive cross-sectional and from a social perspective. The cost-of-illness method, based on the human capital theory, has been used. Both direct and indirect costs have been estimated using a prevalence approach and bottom-up method. Hospital costs were extracted from patients' records and the accounting system of Namazi Hospital. Outpatient expenses were obtained according to the number of outpatient visits and the average cost of visit were obtained by interviewing patients. Socio-economic status, medical expenses and number of days absent from work were determined using a valid and reliable questionnaire. Assessment of the cost of hospital care was made on the basis of the average daily. Non-medical direct costs such as transportation and residence, etc. were also calculated.The total annual economic costs of IBD per patient were estimated at 1229.74 USD. Finally, increased use of health care as well as lost productivity leads to increased disease costs.IBD imposes a substantial economic burden on patients, families and the society. Establishing a correct diagnosis early, management of IBD worsening, and appropriate treatment can reduce the costs of treatment and lost production to some extent. Therefore, policymakers should take this into consideration and according to available health resources, provide services and facilities for the prevention and treatment of the disease.© 2023 The Author(s). This is an open-access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. -raw_completion_output: |- - genes: N/A - exposures: N/A - gene_exposures_relationships: N/A - diseases: Inflammatory bowel disease (IBD) - cellular_process: N/A - disease_cellular_process_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - subject: - predicate: - object: - qualifier: - subject_qualifier: - object_qualifier: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - N/A - gene_exposures_relationships: - - subject: N/A - predicate: N/A - object: N/A - qualifier: N/A - subject_qualifier: N/A - object_qualifier: N/A - diseases: - - MONDO:0005052 - cellular_process: - - N/A - disease_cellular_process_relationships: - - subject: N/A - predicate: N/A - object: N/A - qualifier: N/A - subject_qualifier: N/A - object_qualifier: N/A -named_entities: - - id: MONDO:0005052 - label: Inflammatory bowel disease (IBD) diff --git a/long_output.yaml b/long_output.yaml deleted file mode 100644 index 5a32e1bb0..000000000 --- a/long_output.yaml +++ /dev/null @@ -1,2873 +0,0 @@ -input_text: |- - Title: Relationship between disease activity index and sleep disorders in children with inflammatory bowel diseases. - Abstract: The aim of the study was to assess the prevalence of sleep disturbance in pediatric IBD patients and evaluate the relationship between clinical features of IBD, disease activity, inflammatory markers and quality of sleep. A total of 99 patients who were followed-up with the diagnosis of IBD (44 Crohn's disease (CD), 55 Ulcerative colitis (UC)) between 2015-2020 and 80 healthy controls were enrolled in the study. The clinical and demographic characteristics, laboratory parameters and disease activities were obtained from medical reports retrospectively. Pittsburgh sleep quality index (PSQI) was administered to all participants. PSQI score was significantly higher in patient group than the control group (P < 0.001). The sleep time of patient group, especially patients with UC was later than the control group (P = 0.008). Sleep duration was longer in control group than the patient group (P < 0.001). A positive strong correlation was obtained in disease activity index (r = 0.886; P < 0.001) and abdominal pain (r = 0.781; P < 0.001) with PSQI scores of CD patients. Disease activity index, rectal bleeding, diarrhea and number of stool had statistically significant positive strong correlation with PSQI scores of UC patients (P < 0.001). Pediatric Crohn's disease activity index and Pediatric ulcerative colitis activity index were the only independent risk factors affecting sleep disturbances (80% sensitivity and 91.67% specificity, 93.1% sensitivity and %96.15 specificity, respectively).   Conclusion: Increased disease activity has adverse effects on sleep quality. PSQI and PCDAI were strong tests for predicting sleep disorders in pediatric patients with IBD. What is Known: • Sleep disturbances are common complaint in inflammatory bowel disease (IBD), even in clinical remission. • Pittsburgh sleep quality index (PSQI) was used to evaluate the subjective sleep quality of patients. What is New: • PSQI and Pediatric Crohn Disease Activity index (PCDAI) were strong tests for predicting sleep disorders in pediatric patients with IBD. • PSQI and PCDAI scores correlated significantly with the severity of the sleep disturbances.© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature. - Keywords: Children; Crohn’s disease; Inflammatory bowel disease; Pittsburgh sleep quality index; Ulcerative colitis -raw_completion_output: |- - genes: None mentioned in the text - exposures: disease activity; inflammatory markers - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - disease activity - - inflammatory markers - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Current and Emerging Targeted Therapies for Ulcerative Colitis. - Abstract: Ulcerative colitis is one of the main entities of inflammatory bowel diseases. The clinical course of this immune-mediated disorder is marked by unpredictable exacerbations and asymptomatic remission, causing lifelong morbidity. Optimized anti-inflammatory treatment is a prerequisite to not only restore the quality of life of the affected patients but also halt progressive bowel damage and reduce the risk for colitis-associated neoplasia. Advances in understanding the underlying immunopathogenesis of ulcerative colitis have led to the advent of targeted therapies that selectively inhibit crucial molecular structures or signaling pathways that perpetuate the inflammatory reaction.We will delineate the mode of action and summarize efficacy and safety data of current and emerging targeted therapies in ulcerative colitis, which encompasses representatives of the drug classes of antibodies, small molecules, and oligonucleotides. These substances have already been approved for induction and maintenance treatment or are being tested in late-stage clinical trials in moderately-to-severely active ulcerative colitis patients. These advanced therapies have enabled us to define and achieve novel therapeutic outcomes, such as clinical and endoscopic remission, histological remission, mucosal healing, and recently, also barrier healing as an emerging outcome measure.Established and emerging targeted therapies and monitoring modalities broaden our therapeutic armamentarium and have enabled us to define novel therapeutic outcomes that have the potential to modify the individual disease course of patients with ulcerative colitis.© 2023 S. Karger AG, Basel. - Keywords: Anti-tumor necrosis factor antibody; IL-23; Molecular resistance; Therapy; Ulcerative colitis -raw_completion_output: |- - genes: IL-23 - exposures: Anti-tumor necrosis factor antibody - gene_exposures_relationships: IL-23 to Anti-tumor necrosis factor antibody -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - IL-23 to Anti-tumor necrosis factor antibody - - === - -extracted_object: - genes: - - HGNC:15488 - exposures: - - Anti-tumor necrosis factor antibody - gene_exposures_relationships: - - molecular_activity: IL-23 - gene: Anti-tumor necrosis factor antibody -named_entities: - - id: HGNC:15488 - label: IL-23 -input_text: |- - Title: Intrahepatic cholangiocarcinoma in patients with primary sclerosing cholangitis and ulcerative colitis: Two case reports. - Abstract: Primary sclerosing cholangitis (PSC) is an extraintestinal manifestation of ulcerative colitis (UC). PSC is a well-known risk factor for intrahepatic cholangiocarcinoma (ICC), and ICC is known to have a poor prognosis.We present two cases of ICC in patients with PSC associated with UC. In the first case, a tumor was found by magnetic resonance imaging (MRI) in the liver of a patient with PSC and UC who presented to our hospital with right-sided rib pain. The second patient was asymptomatic, but we unexpectedly detected two liver tumors in an MRI performed to evaluate bile duct stenosis associated with PSC. ICC was strongly suspected by computed tomography and MRI in both cases, and surgery was performed, but unfortunately, the first patient died of ICC recurrence 16 mo postoperatively, and the second patient died of liver failure 14 mo postoperatively.Careful follow-up of patients with UC and PSC with imaging and blood tests is necessary for early detection of ICC.©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved. - Keywords: Case report; Hepatic lobectomy; Inflammatory bowel disease; Intrahepatic cholangiocarcinoma; Primary sclerosing cholangitis; Ulcerative colitis -raw_completion_output: |- - genes: None mentioned in the text - exposures: primary sclerosing cholangitis (PSC), ulcerative colitis (UC) - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - primary sclerosing cholangitis (PSC), ulcerative colitis (UC) - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Surgical management of duodenal Crohn's disease. - Abstract: The case of Crohn's disease involving the duodenum is rare, and its surgical management requires a thorough understanding.To investigate the surgical management of duodenal Crohn's disease.We systematically reviewed patients diagnosed with duodenal Crohn's disease who underwent surgery in the Department of Geriatrics Surgery of the Second Xiangya Hospital of Central South University from January 1, 2004, to August 31, 2022. The general information, surgical procedures, prognosis, and other information of these patients were collected and summarized.A total of 16 patients were diagnosed with duodenal Crohn's disease, where 6 cases had primary duodenal Crohn's disease, and 10 had secondary duodenal Crohn's disease. Among patients with primary disease, 5 underwent duodenal bypass and gastrojejunostomy, and 1 received pancreaticoduodenectomy. Among those with a secondary disease, 6 underwent closure of duodenal defect and colectomy, 3 received duodenal lesion exclusion and right hemicolectomy, and 1 underwent duodenal lesion exclusion and double-lumen ileostomy.Crohn's disease involving the duodenum is a rare condition. Different surgical management should be applied for patients with Crohn's disease presenting with different clinical manifestations.©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved. - Keywords: Crohn’s disease; Duodenum; Inflammatory bowel disease; Surgical treatment -raw_completion_output: |- - genes: N/A - exposures: surgical management - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - surgical management - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: Editorial: Game changers in inflammatory bowel diseases, volume II. - Abstract: - Keywords: EIM; IBD; markers; systemic inflammation; tailored therapy -raw_completion_output: 'genes: Not mentioned in the text' -prompt: |+ - From the text below, extract the following entities in the following format: - - genes: - exposures: - gene_exposures_relationships: - - - Text: - Title: Editorial: Game changers in inflammatory bowel diseases, volume II. - Abstract: - Keywords: EIM; IBD; markers; systemic inflammation; tailored therapy - - === - -extracted_object: - genes: - - Not mentioned in the text -input_text: |- - Title: Administration of Bifidobacterium pseudolongum suppresses the increase of colonic serotonin and alleviates symptoms in dextran sodium sulfate-induced colitis in mice. - Abstract: Previous studies suggested that altered gut serotonin (5-HT) signaling is implicated in the pathophysiology of inflammatory bowel disease (IBD). Indeed, 5-HT administration reportedly exacerbated the severity of murine dextran sodium sulfate (DSS)-induced colitis that mimics human IBD. Our recent study suggested that Bifidobacterium pseudolongum, one of the most predominant bifidobacterial species in various mammals, reduces the colonic 5-HT content in mice. The present study thus tested whether the administration of B. pseudolongum prevents DSS-induced colitis in mice. Colitis was induced by administering 3% DSS in drinking water in female BALB/c mice, and B. pseudolongum (109 CFU/day) or 5-aminosalicylic acid (5-ASA, 200 mg/kg body weight) was intragastrically administered once daily throughout the experimental period. B. pseudolongum administration reduced body weight loss, diarrhea, fecal bleeding, colon shortening, spleen enlargement, and colon tissue damage and increased colonic mRNA levels of cytokine genes (Il1b, Il6, Il10, and Tnf) almost to an extent similar to 5-ASA administration in DSS-treated mice. B. pseudolongum administration also reduced the increase of colonic 5-HT content, whereas it did not alter the colonic mRNA levels of genes that encode the 5-HT synthesizing enzyme, 5-HT reuptake transporter, 5-HT metabolizing enzyme, and tight junction-associated proteins. We propose that B. pseudolongum is as beneficial against murine DSS-induced colitis as the widely used anti-inflammatory agent 5-ASA. However, further studies are needed to clarify the causal relationship between the reduced colonic 5-HT content and reduced severity of DSS-induced colitis caused by B. pseudolongum administration.©2023 BMFH Press. - Keywords: Bifidobacterium pseudolongum; dextran sodium sulfate (DSS)-induced colitis; erotonin; inflammation -raw_completion_output: |- - genes: Il1b; Il6; Il10; Tnf - exposures: Bifidobacterium pseudolongum; dextran sodium sulfate (DSS); 5-aminosalicylic acid (5-ASA) - gene_exposures_relationships: Bifidobacterium pseudolongum - reduction of colonic 5-HT content; Bifidobacterium pseudolongum - prevention of DSS-induced colitis -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - Bifidobacterium pseudolongum - prevention of DSS-induced colitis - - === - -extracted_object: - genes: - - HGNC:5992 - - HGNC:6018 - - HGNC:5962 - - HGNC:11892 - exposures: - - Bifidobacterium pseudolongum - - dextran sodium sulfate (DSS) - - 5-aminosalicylic acid (5-ASA) - gene_exposures_relationships: - - molecular_activity: reduction - gene: colonic 5-HT - - molecular_activity: prevention of DSS-induced colitis - gene: Bifidobacterium pseudolongum -named_entities: - - id: HGNC:5992 - label: Il1b - - id: HGNC:6018 - label: Il6 - - id: HGNC:5962 - label: Il10 - - id: HGNC:11892 - label: Tnf -input_text: |- - Title: A Systematic Review of Self-Management Interventions for Patients with Inflammatory Bowel Disease. - Abstract: Previous studies have reported the effectiveness of inflammatory bowel disease (IBD) self-management. However, it is unclear which types of self-management interventions are effective. We conducted a systematic literature review to clarify the status and efficacy of self-management interventions for IBD.Searches were performed in databases including Embase, Medline, and Cochrane Library. Randomized, controlled studies of interventions in adult human participants with IBD involving a self-management component published in English from 2000 to 2020 were included. Studies were stratified based on study design, baseline demographic characteristics, methodological quality, and how outcomes were measured and analyzed for statistically significant improvements in outcomes, such as psychological health, quality of life, and healthcare resource usage.Among 50 studies included, 31 considered patients with IBD and 14 and 5 focused on patients with ulcerative colitis and Crohn's disease, respectively. Improvements in an outcome were reported in 33 (66%) studies. Most of the interventions that significantly improved an outcome index were based on symptom management and many of these were also delivered in combination with provision of information. We also note that among effective interventions, many were conducted with individualized and patient-participatory activities, and multidisciplinary healthcare practitioners were responsible for delivery of the interventions.Ongoing interventions that focus on symptom management with provision of information may support self-management behavior in patients with IBD. A participatory intervention targeting individuals was suggested to be an effective intervention method.© 2023 The Author(s). Published by S. Karger AG, Basel. - Keywords: Inflammatory bowel disease; Quality of life; Remote monitoring; Self-management; Symptom management -raw_completion_output: |- - genes: Not mentioned - exposures: Not mentioned - gene_exposures_relationships: Not mentioned -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Not mentioned - - === - -extracted_object: - genes: - - Not mentioned - exposures: - - Not mentioned - gene_exposures_relationships: - - molecular_activity: Not mentioned - gene: Not mentioned -input_text: |- - Title: Construction of an Explanatory Model for Quality of Life in Outpatients with Ulcerative Colitis. - Abstract: To date, no studies have reported explanatory models of health-related quality of life (HRQoL) in patients with ulcerative colitis. Therefore, this study aimed to examine HRQoL and its related factors in outpatients with ulcerative colitis to construct an explanatory model.We conducted a cross-sectional survey at a clinic in Japan. The HRQoL was evaluated using the 32-item Inflammatory Bowel Disease Questionnaire. We extracted explanatory variables of HRQoL from demographic, physical, psychological, and social factors reported in previous studies and created a predictive explanatory model. The relationship between explanatory variables and the questionnaire total score was examined using Spearman's rank correlation coefficient, the Mann-Whitney test, or the Kruskal-Wallis test. We conducted multiple regression and path analyses to examine the effect of explanatory variables on the total score.We included 203 patients. Variables that were associated with the total score were the partial Mayo score (r = -0.451), treatment side effects (p = 0.004), the Hospital Anxiety and Depression Scale-Anxiety score (r = -0.678), the Hospital Anxiety and Depression Scale-Depression score (r = -0.528), and the availability of an advisor during difficult times (p = 0.001). The model included the partial Mayo score, treatment side effects, the Hospital Anxiety and Depression Scale-Anxiety score, and the availability of an advisor during difficult times as explanatory variables of the total score that showed the best goodness-of-fit (adjusted R2 = 0.597). The anxiety score exerted the greatest negative effect on the questionnaire total score (β = -0.586), followed by the partial Mayo score (β = -0.373), treatment side effects (β = 0.121), and availability of an advisor during difficult times (β = -0.101).Psychological symptoms exerted the strongest direct effect on HRQoL in outpatients with ulcerative colitis and mediated the relationship between social support and HRQoL. Nurses should listen carefully to the concerns and anxieties of patients to ensure that a social support system is provided by leveraging multidisciplinary collaborations.© 2023 The Author(s). Published by S. Karger AG, Basel. - Keywords: Psychological symptoms; Quality of life; Ulcerative colitis -raw_completion_output: |- - genes: - - exposures: - - gene_exposures_relationships: -prompt: |+ - From the text below, extract the following entities in the following format: - - genes: - exposures: - gene_exposures_relationships: - - - Text: - Title: Construction of an Explanatory Model for Quality of Life in Outpatients with Ulcerative Colitis. - Abstract: To date, no studies have reported explanatory models of health-related quality of life (HRQoL) in patients with ulcerative colitis. Therefore, this study aimed to examine HRQoL and its related factors in outpatients with ulcerative colitis to construct an explanatory model.We conducted a cross-sectional survey at a clinic in Japan. The HRQoL was evaluated using the 32-item Inflammatory Bowel Disease Questionnaire. We extracted explanatory variables of HRQoL from demographic, physical, psychological, and social factors reported in previous studies and created a predictive explanatory model. The relationship between explanatory variables and the questionnaire total score was examined using Spearman's rank correlation coefficient, the Mann-Whitney test, or the Kruskal-Wallis test. We conducted multiple regression and path analyses to examine the effect of explanatory variables on the total score.We included 203 patients. Variables that were associated with the total score were the partial Mayo score (r = -0.451), treatment side effects (p = 0.004), the Hospital Anxiety and Depression Scale-Anxiety score (r = -0.678), the Hospital Anxiety and Depression Scale-Depression score (r = -0.528), and the availability of an advisor during difficult times (p = 0.001). The model included the partial Mayo score, treatment side effects, the Hospital Anxiety and Depression Scale-Anxiety score, and the availability of an advisor during difficult times as explanatory variables of the total score that showed the best goodness-of-fit (adjusted R2 = 0.597). The anxiety score exerted the greatest negative effect on the questionnaire total score (β = -0.586), followed by the partial Mayo score (β = -0.373), treatment side effects (β = 0.121), and availability of an advisor during difficult times (β = -0.101).Psychological symptoms exerted the strongest direct effect on HRQoL in outpatients with ulcerative colitis and mediated the relationship between social support and HRQoL. Nurses should listen carefully to the concerns and anxieties of patients to ensure that a social support system is provided by leveraging multidisciplinary collaborations.© 2023 The Author(s). Published by S. Karger AG, Basel. - Keywords: Psychological symptoms; Quality of life; Ulcerative colitis - - === - -extracted_object: {} -input_text: |- - Title: Smoking Is Not an Independent Risk Factor for Surgery in Patients with Crohn's Disease on Biologic Therapy. - Abstract: The development and course of inflammatory bowel disease appear to be influenced by environmental factors. Particularly, smoking has been shown to assume a harmful role in Crohn's disease (CD) and a protective role in ulcerative colitis. This study aims to examine the effect of smoking on need for surgery in patients with moderate to severe CD receiving biologic therapy.This was a retrospective study of adult patients with CD at a University Medical Center over a 20-year period.A total of 251 patients were included (mean age 36.0 ± 15.0; 70.1% males; current, former, and nonsmokers: 44.2%, 11.6%, and 43.8%, respectively). Mean duration on biologics was 5.0 ± 3.1 years (>2/3 received anti-TNFs, followed by ustekinumab in 25.9%) and a third of patients (29.5%) received more than one biologic. Disease-related surgeries (abdominal, perianal, or both) occurred in 97 patients (38.6%): 50 patients had surgeries prior to starting biologics only, 41 had some surgeries after, and 6 had insufficient information. There was no significant difference in surgeries between ever-smokers (current or previous) versus nonsmokers in the overall study group. On logistic regression, the odds of having any CD surgery were higher in patients with longer disease duration (OR = 1.05, 95% CI = 1.01, 1.09) and in those receiving more than one biologic (OR = 2.31, 95% CI = 1.16, 4.59). However, among patients who had surgery prior to biologic therapy, smokers were more likely to have perianal surgery compared to nonsmokers (OR = 10.6, 95% CI = 2.0, 57.4; p = 0.006).In biologic-naive CD patients requiring surgery, smoking is an independent predictor of perianal surgery. Smoking, however, is not an independent risk factor for surgery in this cohort after starting biologics. The risk of surgery in those patients is primarily associated with disease duration and the use of more than one biologic.© 2023 The Author(s). Published by S. Karger AG, Basel. - Keywords: Abdominal surgery; Adalimumab; Anti-Tumor necrosis factor; Crohn’s disease; Fistula; Infliximab; Perianal; Tobacco; Ustekinumab; Vedolizumab -raw_completion_output: |- - genes: None mentioned in the text. - exposures: smoking - gene_exposures_relationships: None mentioned in the text. -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text. - - === - -extracted_object: - genes: - - None mentioned in the text. - exposures: - - NCIT:C154329 - gene_exposures_relationships: - - molecular_activity: None mentioned in the text. - gene: None mentioned in the text. -named_entities: - - id: NCIT:C154329 - label: smoking -input_text: |- - Title: Gene-based microbiome representation enhances host phenotype classification. - Abstract: With the concomitant advances in both the microbiome and machine learning fields, the gut microbiome has become of great interest for the potential discovery of biomarkers to be used in the classification of the host health status. Shotgun metagenomics data derived from the human microbiome is composed of a high-dimensional set of microbial features. The use of such complex data for the modeling of host-microbiome interactions remains a challenge as retaining de novo content yields a highly granular set of microbial features. In this study, we compared the prediction performances of machine learning approaches according to different types of data representations derived from shotgun metagenomics. These representations include commonly used taxonomic and functional profiles and the more granular gene cluster approach. For the five case-control datasets used in this study (Type 2 diabetes, obesity, liver cirrhosis, colorectal cancer, and inflammatory bowel disease), gene-based approaches, whether used alone or in combination with reference-based data types, allowed improved or similar classification performances as the taxonomic and functional profiles. In addition, we show that using subsets of gene families from specific functional categories of genes highlight the importance of these functions on the host phenotype. This study demonstrates that both reference-free microbiome representations and curated metagenomic annotations can provide relevant representations for machine learning based on metagenomic data. IMPORTANCE Data representation is an essential part of machine learning performance when using metagenomic data. In this work, we show that different microbiome representations provide varied host phenotype classification performance depending on the dataset. In classification tasks, untargeted microbiome gene content can provide similar or improved classification compared to taxonomical profiling. Feature selection based on biological function also improves classification performance for some pathologies. Function-based feature selection combined with interpretable machine learning algorithms can generate new hypotheses that can potentially be assayed mechanistically. This work thus proposes new approaches to represent microbiome data for machine learning that can potentiate the findings associated with metagenomic data. - Keywords: endocannabinoidome; feature selection; gene clusters; gut-brain axis; interpretable models; machine learning; metabolic health; metagenomics; microbiome; shotgun microbiome -raw_completion_output: |- - genes: gene-based approaches, gene families - exposures: gut microbiome, taxonomic and functional profiles, gene cluster approach, reference-based data types, metagenomic annotations, metagenomic data - gene_exposures_relationships: reference-based data types - gene-based approaches; gene families - specific functional categories of genes -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - gene families - specific functional categories of genes - - === - -extracted_object: - genes: - - gene-based approaches, gene families - exposures: - - gut microbiome, taxonomic and functional profiles, gene cluster approach, reference-based - data types, metagenomic annotations, metagenomic data - gene_exposures_relationships: - - molecular_activity: reference-based data types - gene: gene-based approaches - - molecular_activity: specific functional categories of genes - gene: gene families -input_text: |- - Title: Development of the intestinal microbiome in cystic fibrosis in early life. - Abstract: Cystic fibrosis (CF) is a heritable disease that causes altered physiology at mucosal sites; these changes result in chronic infections in the lung, significant gastrointestinal complications as well as dysbiosis of the gut microbiome, although the latter has been less well explored. Here, we describe the longitudinal development of the gut microbiome in a cohort of children with CF (cwCF) from birth through early childhood (0-4 years of age) using 16S rRNA gene amplicon sequencing of stool samples as a surrogate for the gut microbiota. Similar to healthy populations, alpha diversity of the gut microbiome increases significantly with age, but diversity plateaus at ~2 years of age for this CF cohort. Several taxa that have been associated with dysbiosis in CF change with age toward a more healthy-like composition; notable exceptions include Akkermansia, which decreases with age, and Blautia, which increases with age. We also examined the relative abundance and prevalence of nine taxa associated with CF lung disease, several of which persist across early life, highlighting the possibility of the lung being seeded directly from the gut early in life. Finally, we applied the Crohn's Dysbiosis Index to each sample, and found that high Crohn's-associated dysbiosis early in life (<2 years) was associated with significantly lower Bacteroides in samples collected from 2 to 4 years of age. Together, these data comprise an observational study that describes the longitudinal development of the CF-associated gut microbiota and suggest that early markers associated with inflammatory bowel disease may shape the later gut microbiota of cwCF. IMPORTANCE Cystic fibrosis is a heritable disease that disrupts ion transport at mucosal surfaces, causing a buildup of mucus and dysregulation of microbial communities in both the lungs and the intestines. Persons with CF are known to have dysbiotic gut microbial communities, but the development of these communities over time beginning at birth has not been thoroughly studied. Here, we describe an observation study following the development of the gut microbiome of cwCF throughout the first 4 years of life, during the critical window of both gut microbiome and immune development. Our findings indicate the possibility of the gut microbiota as a reservoir of airway pathogens and a surprisingly early indication of a microbiota associated with inflammatory bowel disease. - Keywords: Crohn’s disease; cystic fibrosis; gut; microbiome -raw_completion_output: |- - genes: N/A - exposures: Crohn's disease; cystic fibrosis - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - Crohn's disease - - cystic fibrosis - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: Frail Phenotype in Patients With Inflammatory Bowel Disease. - Abstract: - Keywords: -raw_completion_output: |- - genes: - exposures: - gene_exposures_relationships: -prompt: |+ - From the text below, extract the following entities in the following format: - - genes: - exposures: - gene_exposures_relationships: - - - Text: - Title: Frail Phenotype in Patients With Inflammatory Bowel Disease. - Abstract: - Keywords: - - === - -extracted_object: {} -input_text: |- - Title: Physical activity, quality of diet and bone mineral density in patients with inflammatory bowel disease. - Abstract: The aim of this study was to find an association between moderate, vigorous and total physical activity (PA); diet quality; and bone mineral density (BMD) among patients suffering from inflammatory bowel disease (IBD).We enrolled 54 IBD patients, including those with Crohn's disease (CD) and ulcerative colitis (UC), and 24 healthy adults. All subjects completed the Questionnaire of Eating Behaviour based on which prohealthy and nonhealthy diet indexes were calculated, and the questionnaire included questions from the International Physical Activity Questionnaire. Prohealthy and nonhealthy diet indexes were divided into low-, medium- and high scores. BMD and T- and Z-scores of the lumbar spine (L1-L4) and femoral neck (FN) were assessed using dual-energy X-ray absorptiometry method.BMD, T- and Z-scores of the FN and the Z-score of L1-L4 were significantly lower among patients with CD and UC than healthy controls. We did not find any differences in the time of PA among CD, UC and control groups (CG). The prohealthy diet index was higher among healthy subjects than the CD and UC groups. The nonhealthy diet index was lower among UC patients compared with the CG or CD patients. Prohealthy diet index positively correlated with BMD and T- and Z-scores of L1-L4 and FN in IBD. The prohealthy diet index correlated negatively with C-reactive protein and positively with body mass index. The prohealthy diet index correlated only with total PA in the CD group.A well-balanced diet and proper PA may decrease the risk of osteoporosis in IBD, so education of patients referring to nutrition and PA is needed.© 2023 British Dietetic Association. - Keywords: bone mineral density; diet quality; inflammatory bowel disease; osteoporosis; physical activity -raw_completion_output: |- - genes: N/A - exposures: diet quality; physical activity - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - diet quality - - NCIT:C17708 - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -named_entities: - - id: NCIT:C17708 - label: physical activity -input_text: |- - Title: Sweet Syndrome Associated with Active Inflammatory Bowel Disease: A Case Series of a Rare Extra-intestinal Manifestation. - Abstract: Cutaneous extra-intestinal manifestations (EIM) occur in up to 20% of patients with IBD. Information about Sweet syndrome (SS)'s clinical course as a rare cutaneous EIM in IBD is limited to case reports. We present the largest retrospective cohort on the occurrence and management of SS in IBD.Electronic medical records and paper charts since 1980 were retrospectively reviewed at a large quaternary medical center to identify all adult IBD patients with histopathology-proven SS. Patient characteristics and clinical outcomes were evaluated.25 IBD patients with SS were identified; 3 patients were assessed to have AZA-induced SS. The majority of SS patients were female. Median age at diagnosis was 47 years (IQR 33-54 years) and SS appeared at a median of 6.4 years after IBD diagnosis. IBD patients with SS had a high rate of complicated IBD phenotypes (75% extensive colitis in UC and 73% stricturing or penetrating disease in CD, with 100% colonic involvement), as well as frequent co-occurring EIMs (60%). SS correlated with global IBD disease activity. Corticosteroids were an effective therapy for SS in IBD. Recurrence rate of SS was 36%.Contrary to previous case reports, SS was a cutaneous EIM occurring late after diagnosis of IBD in our cohort, with occurrences paralleling global IBD disease activity. Although AZA-induced and IBD-associated SS were both effectively treated with corticosteroids, distinguishing them is relevant for future IBD treatment strategies.© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature. - Keywords: Azathioprine; Colitis; Cutaneous manifestations; Extra-intestinal manifestation; Inflammatory bowel disease; Sweet syndrome -raw_completion_output: |- - genes: Not mentioned in the text - exposures: Azathioprine - gene_exposures_relationships: Azathioprine -> Sweet syndrome -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Azathioprine -> Sweet syndrome - - === - -extracted_object: - genes: - - Not mentioned in the text - exposures: - - Azathioprine - gene_exposures_relationships: - - molecular_activity: Azathioprine - gene: Sweet syndrome -input_text: |- - Title: Decreased Risk of Preeclampsia in Women with Inflammatory Bowel Disease on Anti-Tumor Necrosis Factor Therapy. - Abstract: Evidence suggests that upregulation of tumor necrosis factor-alpha (TNF-α) plays a role in immune dysregulation in both preeclampsia and inflammatory bowel disease (IBD).We aimed to investigate whether anti-TNF therapy during pregnancy decreases the risk of preeclampsia in women with IBD.The study population included women with IBD and pregnancies who were followed at a tertiary care center from 2007 to 2021. Cases of preeclampsia were compared with controls with a normotensive pregnancy. Data on patient demographics, disease type and activity, pregnancy complications, and additional risk factors for preeclampsia were collected. The association between anti-TNF therapy and preeclampsia was analyzed using univariate analysis and multivariate logistic regression.Women with preeclampsia were more likely to have a preterm delivery (44% vs. 12%, p < 0.001). More women without preeclampsia were exposed to anti-TNF therapy during pregnancy than women with preeclampsia (55% vs. 30%, p = 0.029). The majority of women (32/44) on anti-TNF therapy, either adalimumab or infliximab, continued to have some degree of exposure during the third trimester. Though not significant, multivariate analysis showed a trend towards a protective effect of anti-TNF therapy against developing preeclampsia if exposed during the third trimester (OR 0.39; 95% CI 0.14-1.12, p = 0.08).In this study, anti-TNF therapy exposure was higher in IBD patients who did not develop preeclampsia than in those who did. While not significant, there was a trend towards a protective effect of anti-TNF therapy against preeclampsia if exposed during the third trimester.© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature. - Keywords: Anti-TNF; Crohn’s disease; Inflammatory bowel disease; Preeclampsia; Pregnancy; TNF-α; Ulcerative colitis -raw_completion_output: |- - genes: TNF-α - - exposures: anti-TNF therapy - - gene_exposures_relationships: TNF-α to anti-TNF therapy -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - TNF-α to anti-TNF therapy - - === - -extracted_object: - genes: - - TNF-α - exposures: - - anti-TNF therapy - gene_exposures_relationships: - - molecular_activity: TNF-α - gene: anti-TNF therapy -input_text: |- - Title: Inflammatory bowel disease is not linked to a higher rate of adverse events in colonoscopy - a nationwide population-based study in Sweden. - Abstract: Inflammatory bowel disease may cause long-standing inflammation and fibrosis and may increase the risk of adverse events in colonoscopy. We evaluated whether inflammatory bowel disease and other potential risk factors are associated with bleeding or perforation in a nationwide population-based Swedish study.Data from 969,532 colonoscopies, including 164,012 (17%) on inflammatory bowel disease patients, between 2003 and 2019 were retrieved from the National Patient Registers. ICD-10 codes for bleeding (T810) and perforation (T812) within 30 days of the colonoscopy were recorded. Multivariable logistic regression was used to test if inflammatory bowel disease status, inpatient setting, time period, general anesthesia, age, sex, endoscopic procedures and antithrombotic treatment were associated with higher odds for bleeding and perforation.Bleeding and perforation were reported in 0.19% and 0.11% of all colonoscopies, respectively. Bleeding (Odds Ratio 0.66, p < 0.001) and perforation (Odds Ratio 0.79, p < 0.033) were less likely in colonoscopies in individuals with inflammatory bowel disease status. Bleeding and perforation were more common in inpatient inflammatory bowel disease colonoscopies compared with outpatient. The odds for bleeding but not perforation increased between 2003 to 2019. General anesthesia was associated with double the odds for perforation.Individuals with inflammatory bowel disease did not have more adverse events compared with individuals without inflammatory bowel disease status. However, inpatient setting was associated with more adverse events, especially in inflammatory bowel disease status. General anesthesia was associated with a greater risk of perforation.© The Author(s) 2023. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation. All rights reserved. For permissions, please email: journals.permissions@oup.com. - Keywords: Gastrointestinal Bleeding; Inflammatory Bowel Disease; Perforation -raw_completion_output: |- - genes: - - exposures: inflammatory bowel disease, general anesthesia, antithrombotic treatment - - gene_exposures_relationships: inflammatory bowel disease - bleeding, perforation; general anesthesia - perforation -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - general anesthesia - perforation - - === - -extracted_object: - exposures: - - inflammatory bowel disease, general anesthesia, antithrombotic treatment - gene_exposures_relationships: - - molecular_activity: inflammatory bowel disease - gene: perforation - - molecular_activity: general anesthesia - gene: perforation -input_text: |- - Title: Major Adverse Cardiovascular Events by Baseline Cardiovascular Risk in Patients with Ulcerative Colitis Treated with Tofacitinib: Data from the OCTAVE Clinical Programme. - Abstract: Patients with inflammatory bowel disease have increased risk of atherosclerotic cardiovascular [CV] disease [ASCVD]. Tofacitinib is an oral small molecule Janus kinase inhibitor for treatment of ulcerative colitis [UC]. We report major adverse CV events [MACE] in the UC OCTAVE programme, stratified by baseline CV risk.Rates of MACE were analysed by baseline [first tofacitinib exposure] CV risk profile: prior ASCVD, or 10-year ASCVD risk categories [low, borderline, intermediate, high].Of 1157 patients [2814.4 patient-years' exposure; ≤7.8 years' tofacitinib treatment], 4% had prior ASCVD and 83% had no prior ASCVD and low-borderline baseline 10-year ASCVD risk. Eight patients [0.7%] developed MACE; one had prior ASCVD. Incidence rates [unique patients with events/100 patient-years of exposure; 95% confidence intervals] for MACE were: 0.95 [0.02-5.27] in patients with prior ASCVD; and 1.81 [0.05-10.07], 1.54 [0.42-3.95], 0.00 [0.00-2.85], and 0.09 [0.01-0.32] in patients without prior ASCVD and with high, intermediate, borderline, and low baseline 10year ASCVD risk, respectively. For the 5/7 patients with MACE and without prior ASCVD, 10year ASCVD risk scores were numerically higher [>1%] prior to MACE versus at baseline, primarily due to increasing age.Most patients receiving tofacitinib in the UC OCTAVE programme had low baseline 10-year ASCVD risk. MACE were more frequent in patients with prior ASCVD and higher baseline CV risk. This analysis demonstrates potential associations between baseline CV risk and MACE in patients with UC, suggesting CV risk should be assessed individually in clinical practice.© The Author(s) 2023. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation. - Keywords: cardiovascular risk; inflammatory bowel disease; ulcerative colitis -raw_completion_output: |- - genes: None mentioned in the given text - exposures: Tofacitinib - gene_exposures_relationships: None mentioned in the given text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the given text - - === - -extracted_object: - genes: - - None mentioned in the given text - exposures: - - Tofacitinib - gene_exposures_relationships: - - molecular_activity: None mentioned in the given text - gene: None mentioned in the given text -input_text: |- - Title: Relevance of sonographic parameters for inflammatory bowel disease in children. - Abstract: Intestinal ultrasound (IUS) is widely used as the first exam in patients with suspected inflammatory bowel disease (IBD). This study investigated the accuracy of several IUS parameters, including increased bowel wall thickening (BWT), in detecting IBD in a paediatric population.The study included an unselected series of 113 patients aged 2-18 years (mean age 10.8 years, 65 male), referred for recurrent abdominal pain or altered bowel habits, without known organic diseases, to perform an IUS as first investigation of a diagnostic workup. Patients with full systematic IUS examination, clinical and biochemical exams, and ileocolonoscopy or an uneventful follow-up at least one year follow up were eligible.23 IBD patients (20.4%; 8 ulcerative colitis, 12 Crohn's disease and 3 indeterminate colitis) were diagnosed. We found that increased BWT > 3 mm (OR 5.4), altered IUS bowel pattern (IUS-BP, OR 9.8) and mesenteric hypertrophy (MH, OR 5.2) accurately identified IBD at the multivariate analysis. IUS-BP, MH and BWT > 3 mm had a sensitivity of 78.3%, 65.2% and 69.6% and a specificity of 93.3%, 92.2% and 96.7%, respectively. The combination of these three alterations increased the specificity up to 100%, whilst decreased sensitivity to 56.5%.Among several US parameters suggestive of IBD, the increased BWT, MH and altered echopattern are independent predictors of IBD. The ultrasonographic diagnosis of IBD could be more accurate if relied on combination of different sonographic parameters, than on the sole BWT evaluation.© 2023. The Author(s). - Keywords: Bowel wall thickness; Children; Fecal calprotectin; Inflammatory bowel diseases; Intestinal ultrasound; Ultrasound -raw_completion_output: |- - genes: None mentioned in the text - exposures: Fecal calprotectin - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - Fecal calprotectin - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Fecal acute phase proteins in cats with chronic enteropathies. - Abstract: Chronic enteropathies (CE) are common in cats and reliable biomarkers that can distinguish different causes and predict or monitor response to treatment are currently lacking.To evaluate certain acute phase proteins in feces that could potentially be used as biomarkers in cats with CE.Twenty-eight cats with either inflammatory bowel disease (IBD; n = 13), food-responsive enteropathy (FRE; n = 3) or small cell gastrointestinal lymphoma (SCGL; n = 12) and 29 healthy control cats were prospectively enrolled.Fecal concentrations of haptoglobin, alpha-1-acid-glycoprotein (AGP), pancreatitis-associated protein-1 (PAP-1), ceruloplasmin, and C-reactive protein (CRP) were measured using Spatial Proximity Analyte Reagent Capture Luminescence (SPARCL) immunoassays before and after initiation of treatment. Cats were treated with diet and/or prednisolone (IBD cats), plus chlorambucil (SCGL cats).Compared with controls, median fecal AGP concentrations were significantly lower (25.1 vs 1.8 μg/g; P = .003) and median fecal haptoglobin (0.17 vs 0.5 μg/g), PAP-1 (0.04 vs 0.4 μg/g) and ceruloplasmin (0.15 vs 4.2 μg/g) concentrations were significantly higher (P < .001) in cats with CE. Median fecal AGP concentrations were significantly lower (P = .01) in cats with IBD and FRE (0.6 μg/g) compared with cats with SCGL (10.75 μg/g). A significant reduction was found in CE cats after treatment for median fecal ceruloplasmin concentrations (6.36 vs 1.16 μg/g; P = .04).Fecal AGP concentration shows promise to differentiate cats with SCGL from cats with IBD and FRE. Fecal ceruloplasmin concentrations may be useful to objectively monitor response to treatment in cats with CE.© 2023 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals LLC on behalf of American College of Veterinary Internal Medicine. - Keywords: AGP; PAP-1; ceruloplasmin; fecal biomarkers; haptoglobin -raw_completion_output: |- - genes: - - exposures: PAP-1; ceruloplasmin; haptoglobin; alpha-1-acid-glycoprotein (AGP); C-reactive protein (CRP) - - gene_exposures_relationships: PAP-1 to molecular activity; ceruloplasmin to molecular activity; haptoglobin to molecular activity; alpha-1-acid-glycoprotein (AGP) to molecular activity; C-reactive protein (CRP) to molecular activity -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - C-reactive protein (CRP) to molecular activity - - === - -extracted_object: - exposures: - - PAP-1 - - ceruloplasmin - - haptoglobin - - alpha-1-acid-glycoprotein (AGP) - - C-reactive protein (CRP) - gene_exposures_relationships: - - molecular_activity: PAP-1 - gene: molecular activity - - molecular_activity: exposure to a chemical toxin - gene: ceruloplasmin - - molecular_activity: molecular activity - gene: haptoglobin - - molecular_activity: molecular activity - gene: HGNC:30889 - - molecular_activity: C-reactive protein (CRP) - gene: molecular activity -named_entities: - - id: HGNC:30889 - label: alpha-1-acid-glycoprotein (AGP) -input_text: |- - Title: Does intestinal obstruction influence hypo-albuminemia: assessment of the physio-pathogenesis of protein-losing enteropathy with literature review. - Abstract: Non-steroidal anti-inflammatory drug (NSAID) use may cause diaphragm-like lesions in the bowel. Although NSAID-enteropathy is among the causes of protein-losing enteropathy (PLE), intractable hypoalbuminemia is rare.Here, we discuss a case of NSAID-enteropathy with a diaphragm-like disease that presented with Protein Losing Enteropathy (PLE) rather than obstruction. The hypoalbuminemia recovered immediately after resection of the obstructive segment, despite ongoing annular ulcerations in the early postoperative period. Thus, it was not clear whether obstructive mechanisms influenced resistant hypoalbuminemia besides the ulcers. We also reviewed the English-written literature for "diaphragm-type lesion, NSAID-enteropathy, obstruction, and protein-losing enteropathy". We noted that the role of obstruction in the pathophysiology of PLE was not clear.As our case and a couple of cases reported in literature, slow-onset obstructive pathology seems to contribute to well-known factors: inflammatory response, exudation, tight-junction dysfunction, and increase in permeability in the physiopathology of NSAID-induced PLE. Factors such as distention-induced low-flow ischemia and reperfusion, cholecystectomy-related continuous bile flow, bacterial overgrowth-related bile deconjugation and concomitant inflammation are among other potential influencers. The possible role of a slow-onset obstructive pathology in the physiopathology of NSAID-induced and other PLE needs to be further elucidated. - Keywords: -raw_completion_output: |- - genes: not mentioned in the text - exposures: non-steroidal anti-inflammatory drug (NSAID) - gene_exposures_relationships: not mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - not mentioned in the text - - === - -extracted_object: - genes: - - not mentioned in the text - exposures: - - CHEBI:35475 - gene_exposures_relationships: - - molecular_activity: not mentioned in the text - gene: not mentioned in the text -named_entities: - - id: CHEBI:35475 - label: non-steroidal anti-inflammatory drug (NSAID) -input_text: |- - Title: Comparison of infliximab with adalimumab in biologic-naïve patients with Crohn's disease: a single-center 13-year experience. - Abstract: Long-term comparison studies between infliximab (IFX) and adalimumab (ADA) with or without immunomodulator therapy are still needed in Crohn's disease (CD). In this study, we evaluated IFX and ADA for long-term clinical effectiveness and safety in CD patients who had not previously received a biologic treatment.The data of adult CD patients were collected retrospectively between December 2007 and February 2021. We compared CD-related hospitalization, CD-related abdominal surgery, steroid use, and serious infections.Out of 224 CD patients, 101 started IFX first (median age: 38.12 years, 61.4% male), while 123 started ADA first (median age: 30.2 years, 64.2% male). The disease durations were 7.01 years and 6.91 years for IFX and ADA, respectively. There were no significant differences between the two groups with respect to age, gender, smoking, immunomodulator usage, and disease activity score at the onset of anti-TNF therapy (p>0.05). Overall, the median follow-up time was 2.36 and 1.86 years after starting anti-tumor necrosis factor-alpha (anti-TNF) therapy in the IFX and ADA groups, respectively. Steroid use (4.0% vs. 10.6%, p=0.109), hospitalization for CD (13.9% vs. 22.8%, p=0.127), abdominal surgery for CD (9.9% vs. 13.0%, p=0.608), and major infections (1.0% vs. 0.8%, p>0.999) did not differ significantly from one another. There were also no significant differences in the rates of these outcomes between concomitant immunomodulator therapy and monotherapy (p>0.05).In this study, we observed no significant differences in the long-term effectiveness and safety of IFX and ADA in biologic-naïve patients with CD. - Keywords: -raw_completion_output: |- - genes: IFX, ADA, CD - - exposures: immunomodulator therapy, anti-TNF therapy - - gene_exposures_relationships: IFX - immunomodulator therapy; ADA - immunomodulator therapy; IFX - anti-TNF therapy; ADA - anti-TNF therapy -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - ADA - anti-TNF therapy - - === - -extracted_object: - genes: - - IFX, ADA, CD - exposures: - - immunomodulator therapy, anti-TNF therapy - gene_exposures_relationships: - - molecular_activity: immunomodulator therapy - gene: IFX - - molecular_activity: immunomodulator therapy - gene: HGNC:186 - - molecular_activity: anti-TNF therapy - gene: IFX - - molecular_activity: anti-TNF therapy - gene: HGNC:186 -named_entities: - - id: HGNC:186 - label: ADA -input_text: |- - Title: Disease clearance in ulcerative colitis: Is the ultimate therapeutic target? - Abstract: - Keywords: IBD; gastroenterology; inflammation; inflammatory bowel disease; ulcerative colitis -raw_completion_output: |- - genes: none mentioned - exposures: none mentioned - gene_exposures_relationships: none mentioned -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - none mentioned - - === - -extracted_object: - genes: - - none mentioned - exposures: - - none mentioned - gene_exposures_relationships: - - molecular_activity: none mentioned - gene: none mentioned -input_text: |- - Title: Dissecting the effect of ileal faecal diversion on the intestine using single-cell sequencing. - Abstract: Although ileal faecal diversion is commonly used in clinical settings, complications accompany it. Elucidating the intestinal changes caused by ileal faecal diversion will help resolve postoperative complications and elucidate the pathogenic mechanisms of associated intestinal disorders, such as Crohn's disease (CD). Therefore, our study aimed to provide new insights into the effects of ileal faecal diversion on the intestine and the potential mechanisms.Single-cell RNA sequencing was performed on proximal functional and paired distal defunctioned intestinal mucosae from three patients with ileal faecal diversion. We also performed in vitro cellular and animal experiments, tissue staining and analysed public datasets to validate our findings.We found that the epithelium in the defunctioned intestine tended to be immature, with defective mechanical and mucous barriers. However, the innate immune barrier in the defunctioned intestine was enhanced. Focusing on the changes in goblet cells, we demonstrated that mechanical stimulation promotes the differentiation and maturation of goblet cells through the TRPA1-ERK pathway, indicating that the absence of mechanical stimulation may be the main cause of defects in the goblet cells of the defunctioned intestine. Furthermore, we found obvious fibrosis with a pro-fibrotic microenvironment in the defunctioned intestine and identified that monocytes may be important targets for faecal diversion to alleviate CD.This study revealed the different transcription landscapes of various cell subsets and the potential underlying mechanisms within the defunctioned intestine, when compared to the functional intestine, based on the background of ileal faecal diversion. These findings provide novel insights for understanding the physiological and pathological roles of the faecal stream in the intestine.© 2023 The Authors. Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics. - Keywords: Crohn's disease; TRPA1; fibrosis; ileal faecal diversion; intestinal goblet cells; single-cell RNA sequencing -raw_completion_output: |- - genes: TRPA1 - exposures: ileal faecal diversion - gene_exposures_relationships: TRPA1-ERK pathway; faecal diversion -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - faecal diversion - - === - -extracted_object: - genes: - - HGNC:497 - exposures: - - ileal faecal diversion - gene_exposures_relationships: - - molecular_activity: TRPA1-ERK pathway - gene: None - - molecular_activity: exposure to a chemical toxin. - gene: faecal diversion -named_entities: - - id: HGNC:497 - label: TRPA1 -input_text: |- - Title: Diet high in linoleic acid dysregulates the intestinal endocannabinoid system and increases susceptibility to colitis in Mice. - Abstract: Inflammatory bowel disease (IBD) is a multifactorial disease with increasing incidence in the U.S. suggesting that environmental factors, including diet, are involved. It has been suggested that excessive consumption of linoleic acid (LA, C18:2 omega-6), which must be obtained from the diet, may promote the development of IBD in humans. To demonstrate a causal link between LA and IBD, we show that a high fat diet (HFD) based on soybean oil (SO), which is comprised of ~55% LA, increases susceptibility to colitis in several models, including IBD-susceptible IL10 knockout mice. This effect was not observed with low-LA HFDs derived from genetically modified soybean oil or olive oil. The conventional SO HFD causes classical IBD symptoms including immune dysfunction, increased intestinal epithelial barrier permeability, and disruption of the balance of isoforms from the IBD susceptibility gene Hepatocyte Nuclear Factor 4α (HNF4α). The SO HFD causes gut dysbiosis, including increased abundance of an endogenous adherent invasive Escherichia coli (AIEC), which can use LA as a carbon source. Metabolomic analysis shows that in the mouse gut, even in the absence of bacteria, the presence of soybean oil increases levels of LA, oxylipins and prostaglandins. Many compounds in the endocannabinoid system, which are protective against IBD, are decreased by SO both in vivo and in vitro. These results indicate that a high LA diet increases susceptibility to colitis via microbial and host-initiated pathways involving alterations in the balance of bioactive metabolites of omega-6 and omega-3 polyunsaturated fatty acids, as well as HNF4α isoforms. - Keywords: HNF4α; IBD; PUFAs; adherent invasive E.Coli; epithelial barrier function; gut microbiome; metabolomics; olive oil; oxylipins; soybean oil -raw_completion_output: |- - genes: IL10, Hepatocyte Nuclear Factor 4α (HNF4α) - exposures: linoleic acid (LA), soybean oil (SO), omega-6 and omega-3 polyunsaturated fatty acids, adherent invasive Escherichia coli (AIEC) - gene_exposures_relationships: IL10 - linoleic acid (LA); Hepatocyte Nuclear Factor 4α (HNF4α) - linoleic acid (LA), soybean oil (SO) -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - Hepatocyte Nuclear Factor 4α (HNF4α) - linoleic acid (LA), soybean oil (SO) - - === - -extracted_object: - genes: - - IL10, Hepatocyte Nuclear Factor 4α (HNF4α) - exposures: - - CHEBI:17351 - gene_exposures_relationships: - - molecular_activity: CHEBI:17351 - gene: HGNC:5962 - - molecular_activity: exposure to a chemical toxin. - gene: Hepatocyte Nuclear Factor 4α (HNF4α) -named_entities: - - id: CHEBI:17351 - label: linoleic acid (LA), soybean oil (SO), omega-6 and omega-3 polyunsaturated - fatty acids, adherent invasive Escherichia coli (AIEC) - - id: HGNC:5962 - label: IL10 -input_text: |- - Title: A catalog of bacterial reference genomes from cultivated human oral bacteria. - Abstract: The oral cavity harbors highly diverse communities of microorganisms. However, the number of isolated species and high-quality genomes is limited. Here we present a Cultivated Oral Bacteria Genome Reference (COGR), comprising 1089 high-quality genomes based on large-scale aerobic and anaerobic cultivation of human oral bacteria isolated from dental plaques, tongue, and saliva. COGR covers five phyla and contains 195 species-level clusters of which 95 include 315 genomes representing species with no taxonomic annotation. The oral microbiota differs markedly between individuals, with 111 clusters being person-specific. Genes encoding CAZymes are abundant in the genomes of COGR. Members of the Streptococcus genus make up the largest proportion of COGR and many of these harbor entire pathways for quorum sensing important for biofilm formation. Several clusters containing unknown bacteria are enriched in individuals with rheumatoid arthritis, emphasizing the importance of culture-based isolation for characterizing and exploiting oral bacteria.© 2023. The Author(s). - Keywords: -raw_completion_output: |- - genes: Streptococcus - exposures: quorum sensing - gene_exposures_relationships: Streptococcus-gene expression in quorum sensing -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Streptococcus-gene expression in quorum sensing - - === - -extracted_object: - genes: - - Streptococcus - exposures: - - quorum sensing - gene_exposures_relationships: - - molecular_activity: quorum sensing - gene: Streptococcus -input_text: |- - Title: Letter to Editor in Response to: The Use of Perioperative Nutrition Score in Postoperative Pediatric Inflammatory Bowel Disease. - Abstract: - Keywords: -raw_completion_output: |- - genes: Not mentioned in the text - exposures: Not mentioned in the text - gene_exposures_relationships: Not mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Not mentioned in the text - - === - -extracted_object: - genes: - - Not mentioned in the text - exposures: - - Not mentioned in the text - gene_exposures_relationships: - - molecular_activity: Not mentioned in the text - gene: Not mentioned in the text -input_text: |- - Title: Assessing Serious Infections in Children Exposed In Utero to Ustekinumab. - Abstract: Chronic inflammatory conditions, including inflammatory bowel disease (IBD), psoriasis (PsO), and psoriatic arthritis (PsA), have a high burden among women of reproductive age. There has been significant interest in finding safe ways of controlling disease activity during pregnancy without adversely affecting the pregnancy or offspring. - Keywords: -raw_completion_output: |- - genes: None mentioned in the text - exposures: Ustekinumab - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - Ustekinumab - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Impact of the Affordable Care Act on Providing Equitable Healthcare Access for Inflammatory Bowel Disease in the Kentucky Appalachian Region. - Abstract: Medicaid expansion improved insurance coverage for patients with chronic conditions and low income. The effect of Medicaid expansion on patients with inflammatory bowel disease from high-poverty communities is unknown.This study aimed to evaluate the impact of Medicaid expansion in Kentucky on care for inflammatory bowel disease patients from the Eastern-Kentucky Appalachian community, a historically impoverished area.This study was a retrospective, descriptive, ecological study.This study was conducted in Kentucky using the Hospital Inpatient Discharge and Outpatient Services Database.All encounters for inflammatory bowel disease care for 2009-2020 for patients from the Eastern-Kentucky Appalachian region were included.The primary outcomes measured were proportions of inpatient and emergency encounters, total hospital charge, and hospital length of stay.825 pre-expansion and 5726 post-expansion encounters were identified. Post-expansion demonstrated decreases in the uninsured (9.2% to 1.0%, p < 0.001), inpatient encounters (42.7% to 8.1%, p < 0.001), emergency admissions (36.7% to 12.3%, p < 0.001), admission from the emergency department (8.0% to 0.2%, p < 0.001), median total hospital charge ($7080 to $3260, p < 0.001), and median total hospital length of stay (4 to 3 days, p < 0.001). Similarly, Medicaid coverage (18.8% to 27.7%, p < 0.001), outpatient encounters (57.3% to 91.9%, p < 0.001), elective admissions (46.9% to 76.2%, p < 0.001), admissions from clinic (78.4% to 90.2%, p < 0.001), and discharges to home (43.8% to 88.2%, p < 0.001) increased post-expansion.This study is subject to the limitations inherent of being retrospective and using a partially-deidentified database.This study is the first to demonstrate the changes in trends in care following Medicaid expansion for patients with inflammatory bowel disease in the Commonwealth of Kentucky, especially Appalachian Kentucky, showing significantly increased outpatient care utilization, reduced emergency department encounters, and decreased length of stays.Copyright © The ASCRS 2023. - Keywords: -raw_completion_output: |- - genes: - exposures: Medicaid expansion - gene_exposures_relationships: Medicaid expansion -> improved insurance coverage -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Medicaid expansion -> improved insurance coverage - - === - -extracted_object: - exposures: - - Medicaid expansion - gene_exposures_relationships: - - molecular_activity: Medicaid expansion - gene: improved insurance coverage -input_text: |- - Title: Prognostic role of intestinal ultrasound in Crohn's disease. - Abstract: The majority of patients affected by Crohn's disease (CD) develop a chronic condition with persistent inflammation and relapses that may cause progressive and irreversible damage to the bowel, resulting in stricturing or penetrating complications in around 50% of patients during the natural history of the disease. Surgery is frequently needed to treat complicated disease when pharmacological therapy failes, with a high risk of repeated operations in time. Intestinal ultrasound (IUS), a non-invasive, cost-effective, radiation free and reproducible method for the diagnosis and follow-up of CD, in expert hands, allow a precise assessment of all the disease manifestations: Bowel characteristics, retrodilation, wrapping fat, fistulas and abscesses. Moreover, IUS is able to assess bowel wall thickness, bowel wall stratification (echo-pattern), vascularization and elasticity, as well as mesenteric hypertrophy, lymph-nodes and mesenteric blood flow. Its role in the disease evaluation and behaviour description is well assessed in literature, but less is known about the potential space of IUS as predictor of prognostic factors suggesting response to a medical treatment or postoperative recurrence. The availability of a low cost exam as IUS, able to recognize which patients are more likely to respond to a specific therapy and which patients are at high risk of surgery or complications, could be a very useful instrument in the hands of IBD physician. The aim of this review is to present current evidence about the prognostic role that IUS can show in predicting response to treatment, disease progression, risk of surgery and risk of post-surgical recurrence in CD.©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved. - Keywords: Bowel wall thickness; Crohn’s disease; Intestinal surgery; Intestinal ultrasound; Postoperative recurrence; Remission -raw_completion_output: |- - genes: None mentioned in the text - exposures: Baishideng Publishing Group Inc. - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - Baishideng Publishing Group Inc. - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Spatial cluster mapping and environmental modeling in pediatric inflammatory bowel disease. - Abstract: Geographical (geospatial) clusters have been observed in inflammatory bowel disease (IBD) incidence and linked to environmental determinants of disease, but pediatric spatial patterns in North America are unknown. We hypothesized that we would identify geospatial clusters in the pediatric IBD (PIBD) population of British Columbia (BC), Canada and associate incidence with ethnicity and environmental exposures.To identify PIBD clusters and model how spatial patterns are associated with population ethnicity and environmental exposures.One thousand one hundred eighty-three patients were included from a BC Children's Hospital clinical registry who met the criteria of diagnosis with IBD ≤ age 16.9 from 2001-2016 with a valid postal code on file. A spatial cluster detection routine was used to identify areas with similar incidence. An ecological analysis employed Poisson rate models of IBD, Crohn's disease (CD), and ulcerative colitis (UC) cases as functions of areal population ethnicity, rurality, average family size and income, average population exposure to green space, air pollution, and vitamin-D weighted ultraviolet light from the Canadian Environmental Health Research Consortium, and pesticide applications.Hot spots (high incidence) were identified in Metro Vancouver (IBD, CD, UC), southern Okanagan regions (IBD, CD), and Vancouver Island (CD). Cold spots (low incidence) were identified in Southeastern BC (IBD, CD, UC), Northern BC (IBD, CD), and on BC's coast (UC). No high incidence hot spots were detected in the densest urban areas. Modeling results were represented as incidence rate ratios (IRR) with 95%CI. Novel risk factors for PIBD included fine particulate matter (PM2.5) pollution (IRR = 1.294, CI = 1.113-1.507, P < 0.001) and agricultural application of petroleum oil to orchards and grapes (IRR = 1.135, CI = 1.007-1.270, P = 0.033). South Asian population (IRR = 1.020, CI = 1.011-1.028, P < 0.001) was a risk factor and Indigenous population (IRR = 0.956, CI = 0.941-0.971, P < 0.001), family size (IRR = 0.467, CI = 0.268-0.816, P = 0.007), and summer ultraviolet (IBD = 0.9993, CI = 0.9990-0.9996, P < 0.001) were protective factors as previously established. Novel risk factors for CD, as for PIBD, included: PM2.5 air pollution (IRR = 1.230, CI = 1 .056-1.435, P = 0.008) and agricultural petroleum oil (IRR = 1.159, CI = 1.002-1.326, P = 0.038). Indigenous population (IRR = 0.923, CI = 0.895-0.951, P < 0.001), as previously established, was a protective factor. For UC, rural population (UC IRR = 0.990, CI = 0.983-0.996, P = 0.004) was a protective factor and South Asian population (IRR = 1.054, CI = 1.030-1.079, P < 0.001) a risk factor as previously established.PIBD spatial clusters were identified and associated with known and novel environmental determinants. The identification of agricultural pesticides and PM2.5 air pollution need -raw_completion_output: |- - genes: IBD, CD, UC - exposures: fine particulate matter (PM2.5) pollution, agricultural application of petroleum oil to orchards and grapes - gene_exposures_relationships: IBD - PM2.5 pollution, IBD - agricultural application of petroleum oil to orchards and grapes -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - IBD - PM2.5 pollution, IBD - agricultural application of petroleum oil to orchards and grapes - - === - -extracted_object: - genes: - - IBD, CD, UC - exposures: - - fine particulate matter (PM2.5) pollution, agricultural application of petroleum - oil to orchards and grapes - gene_exposures_relationships: - - molecular_activity: agricultural application of petroleum oil - gene: HGNC:87 -named_entities: - - id: HGNC:87 - label: IBD -input_text: |- - Title: Low vaccination and infection rate of Omicron in patients with inflammatory bowel disease: a comparative study of three unique cohorts. - Abstract: The SARS-CoV-2 Omicron variant caused a large-scale outbreak of COVID-19 in Shanghai, China. Patients with inflammatory bowel disease (IBD) are at high risk of infection due to immunosuppressive interventions. We aimed to investigate the vaccination information of patients with IBD and update a vaccination guide based on a comparison of vaccination in asymptomatic carriers and healthy individuals.This retrospective study was conducted during an Omicron variant wave. We assessed the vaccination status in patients with IBD, asymptomatic carriers and healthy individuals. Factors with unvaccinated status and adverse events following vaccination were also determined in patients with IBD.The vaccination rate was 51.2% in patients with IBD, 73.2% in asymptomatic carriers, and 96.1% in healthy individuals. Female sex (p = 0.012), Crohn's disease (p = 0.026), and disease behavior of B3 (p = 0.029) were factors that indicated a lower vaccination rate. A significantly higher proportion of healthy individuals had received one booster dose (76.8%) than asymptomatic carriers (43.4%) and patients with IBD (26.2%). Patients with IBD received vaccination without an increased risk of adverse events (p = 0.768).The vaccination rate of patients with IBD remains much lower than that of asymptomatic carriers and healthy individuals. The COVID-19 vaccine has been found to be safe among all three groups and patients with IBD are not more susceptible to adverse events.Copyright © 2023 Feng, Yang, Yao, Feng, Hao, Qiao, Tong and Shen. - Keywords: Omicron; asymptomatic; coronavirus disease-19 (COVID-19); inflammatory bowel disease (IBD); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) -raw_completion_output: |- - genes: None mentioned in the text - exposures: Omicron variant, SARS-CoV-2, COVID-19 vaccine - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - Omicron variant, SARS-CoV-2, COVID-19 vaccine - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Inappropriate Multi-Target Stool DNA Use for Colorectal Cancer Screening: Risks, Compliance, and Outcomes. - Abstract: Background Inappropriate or "off-label" use of multi-target stool DNA (mt-sDNA) tests refers to their use in patients for whom colonoscopy or no testing at all is warranted. Examples include a positive family history of colorectal cancer, a history of inflammatory bowel disease, or medical issues necessitating diagnostic colonoscopy, among others. Current understanding of off-label mt-sDNA use for colorectal cancer screening, its associated risks, and outcomes is lacking. We examined off-label mt-sDNA prescription and compliance with testing in an outpatient setting in southeast Michigan. Aims The primary aims of the study were determining the extent of off-label mt-sDNA testing and compliance, and results of all testing, as well as demographic factors associated with off-label prescriptions. The secondary aims were to examine explanations for incomplete testing and factors contributing to successful completion. Methods Using a retrospective design, we identified mt-sDNA orders from outpatient internal medicine clinics between January 1, 2018, to July 31, 2019, to evaluate the proportion of off-label mt-sDNA, results of testing, and follow-up colonoscopies up to one year after order placement. Patients were categorized as "off-label" if any inappropriate criteria were met. Statistical analysis was performed for primary and secondary outcomes. Results From 679 mt-sDNA orders within the study period, 81 (12.1%) had at least one off-label criterion for testing. In total, 404/679 (59.5%) patients completed testing. Lack of follow-up comprised the majority of incompletions (216/275; 78.6%). Only 52 (70.3%) out of 74 positive results were followed by diagnostic colonoscopy. Retired employment status (OR = 1.87; 95%CI, 1.17-2.98; P = 0.008) and age of 76 years or older (OR = 2.28; 95%CI, 0.99-5.21; P = 0.044) were significantly associated with increased risk of off-label mt-sDNA prescription. Increasing age range was associated with higher test completion (χ2 (5) = 12.085, p = 0.034). Multinomial logistic regression revealed an increasing age range (OR = 1.29; 95% CI, 1.09-1.54; P = 0.004), predictive of a positive mt-sDNA result for both groups. There was no significant difference between off-label or on-label groups in the mean number of resected polyps or pathology scores on follow-up colonoscopy. Conclusions Off-label mt-sDNA use remains a concern in the outpatient setting. Compliance for test completion and follow-up colonoscopy for positive results require further improvement. Our findings shed new light on the factors associated with off-label testing while reiterating its burden. We also describe common reasons for incomplete tests in an attempt to augment future colorectal cancer (CRC) screening initiatives.Copyright © 2023, Lazar et al. - Keywords: cologuard®; colon cancer prevention; colon cancer screening; colorectal canc -raw_completion_output: |- - genes: None mentioned - exposures: multi-target stool DNA (mt-sDNA) tests - gene_exposures_relationships: None mentioned -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned - - === - -extracted_object: - genes: - - None mentioned - exposures: - - multi-target stool DNA (mt-sDNA) tests - gene_exposures_relationships: - - molecular_activity: None mentioned - gene: None mentioned -input_text: |- - Title: Protective effects of IRG1/itaconate on acute colitis through the inhibition of gasdermins-mediated pyroptosis and inflammation response. - Abstract: Inflammatory bowel disease (IBD) is a chronic relapsing gastrointestinal disorder, while the treatment effect is not satisfactory. Immune responsive gene 1 (IRG1) is a highly expressed gene in macrophage in response to inflammatory response and catalyzes the production of itaconate. Studies have reported that IRG1/itaconate has a significant antioxidant effect. This study aimed to investigate the effect and mechanism of IRG1/itaconate on dextran sulfate sodium (DSS)-induced colitis in vivo and in vitro. In vivo experiments, we found IRG1/itaconate exerted protective effects against acute colitis by increasing mice weight, the length of colon, reducing disease activity index and colonic inflammation. Meanwhile, IRG1 deletion aggravated the macrophages/CD4+/CD8+ T-cell accumulation, and increased the release of interleukin (IL)-1β, tumor necrosis factor-α (TNF-α), IL-6, the activation of nuclear factor-κB (NF-κB)/mitogen-activated protein kinase (MAPK) signaling pathway, and gasdermin D (GSDMD) mediated pyroptosis. Four-octyl itaconate (4-OI), a derivative of itaconate, attenuated these changes, therefore relieved DSS-induced colitis. In vitro experiment, we found 4-OI inhibited the reactive oxygen species production, thereby inhibiting the activation of MAPK/NF-κB signaling pathway in RAW264.7 and murine bone-marrow-derived macrophages. Simultaneously, we found 4-OI inhibited caspase1/GSDMD-mediated pyroptosis to reduce the release of cytokines. Finally, we found anti-TNF-α agent reduced the severity of DSS-induced colitis and inhibited gasdermin E (GSDME)-mediated pyroptosis in vivo. Meanwhile, our study revealed that 4-OI inhibited caspase3/GSDME-mediated pyroptosis induced by TNF-α in vitro. Taken together, IRG1/itaconate exerted a protective role in DSS-induced colitis by inhibiting inflammatory response and GSDMD/GSDME-mediated pyroptosis, which could be a promising candidate for IBD therapy.© 2022 The Authors. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. - Keywords: Colitis; Gasdermin D; Gasdermin E; IRG1; Inflammation -raw_completion_output: |- - genes: IRG1, GSDMD, GSDME - exposures: itaconate, DSS (dextran sulfate sodium), IL-1β, TNF-α, IL-6, NF-κB (nuclear factor-κB), MAPK (mitogen-activated protein kinase), 4-OI (four-octyl itaconate), caspase1, caspase3 - gene_exposures_relationships: IRG1/itaconate inhibits gasdermin D (GSDMD)-mediated pyroptosis; IRG1/itaconate inhibits gasdermin E (GSDME)-mediated pyroptosis; 4-OI attenuates the effects of DSS-induced colitis; 4-OI inhibits the activation of MAPK/NF-κB signaling pathway; 4-OI inhibits caspase1/GSDMD-mediated pyroptosis; 4-OI inhibits caspase3/GSDME-mediated pyroptosis; TNF-α agent reduces the severity of DSS-induced colitis; TNF-α agent inhibits gasdermin E (GSDME)-mediated pyroptosis. -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - TNF-α agent inhibits gasdermin E (GSDME)-mediated pyroptosis. - - === - -extracted_object: - genes: - - IRG1, GSDMD, GSDME - exposures: - - itaconate, DSS (dextran sulfate sodium), IL-1β, TNF-α, IL-6, NF-κB (nuclear - factor-κB), MAPK (mitogen-activated protein kinase), 4-OI (four-octyl itaconate), - caspase1, caspase3 - gene_exposures_relationships: - - molecular_activity: pyroptosis - gene: HGNC:25697 - - molecular_activity: inhibits gasdermin E (GSDME)-mediated pyroptosis - gene: HGNC:33904 - - molecular_activity: effects - gene: DSS-induced colitis - - molecular_activity: activation - gene: MAPK/NF-κB - - molecular_activity: pyroptosis - gene: HGNC:25697 - - molecular_activity: pyroptosis - gene: caspase3/GSDME - - molecular_activity: DSS-induced colitis - gene: TNF-α agent - - molecular_activity: inhibits - gene: HGNC:2810 -named_entities: - - id: HGNC:25697 - label: GSDMD - - id: HGNC:33904 - label: IRG1 - - id: HGNC:2810 - label: GSDME -input_text: |- - Title: Autophagy in intestinal fibrosis: relevance in inflammatory bowel disease. - Abstract: Chronic inflammation is often associated with fibrotic disorders in which an excessive deposition of extracellular matrix is a hallmark. Long-term fibrosis starts with tissue hypofunction and finally ends in organ failure. Intestinal fibrosis is not an exception, and it is a frequent complication of inflammatory bowel disease (IBD). Several studies have confirmed the link between deregulated autophagy and fibrosis and the presence of common prognostic markers; indeed, both up- and downregulation of autophagy are presumed to be implicated in the progression of fibrosis. A better knowledge of the role of autophagy in fibrosis may lead to it becoming a potential target of antifibrotic therapy. In this review we explore novel advances in the field that highlight the relevance of autophagy in fibrosis, and give special focus to fibrosis in IBD patients.Copyright © 2023 Macias-Ceja, Barrachina and Ortiz-Masià. - Keywords: Crohn’s disease; autophagy; colitis; fibrosis; inflammatory bowel disease; intestinal fibrosis -raw_completion_output: |- - genes: N/A - exposures: autophagy - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - autophagy - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: Provincial variation in colorectal cancer screening adherence in Canada; evidence from the Canadian Partnership for Tomorrow's Health. - Abstract: Although colorectal cancer (CRC) screening program is proven to reduce CRC incidence and mortality, understanding patterns and predictors of suboptimal adherence in screening program requires further investigation in Canada.We used self-reported data from five regional cohorts of the Canadian Partnership for Tomorrow's Health (CanPath), namely the BC Generations Project (BCGP), Alberta's Tomorrow Project (ATP), the Ontario Health Study (OHS), Quebec's CARTaGENE, and the Atlantic Partnership for Tomorrow's Health Study (Atlantic PATH). We stratified participants into the following four risk categories: 1) age 50-74 years, 2) family history in a first-degree relative, 3) personal history of chronic inflammatory bowel disease and/or polyps, and 4) co-existence of personal risk and family history. Multivariable logistic regression was used to identify predictors of adherence to the screening guidelines.Adherence to CRC screening varied considerably between regions, ranging from 16.6% in CARTaGENE to 47.7% in OHS. Compared to the largest cohort OHS, the likelihood of non-adherence to CRC screening was significantly higher in BCGP (OR 1.15, 95% CI 1.11-1.19), the Atlantic PATH (OR 1.90, 95% CI 1.82-1.99) and CARTaGENE (OR 5.10, 95% CI 4.85-5.36). Low physical activity, current smoking, presence of personal risk, family history of CRC significantly reduced the likelihood of adherence to screening recommendations.Compared to the national target of ≥ 60% for participation in CRC screening, adherence to regular CRC screening was suboptimal in this cohort of Canadians and varied by region. Further efforts are needed to identify the specific barriers to screening adherence in different provinces and across risk categories.Copyright © 2023 Darvishian, Moustaqim-Barrette, Awadalla, Bhatti, Broet, McDonald, Murphy, Skead, Urquhart, Vena and Dummer. - Keywords: CanPath cohort; Canada; adherence; colorectal cancer; screening -raw_completion_output: |- - genes: Not mentioned - exposures: None mentioned - gene_exposures_relationships: Not applicable -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Not applicable - - === - -extracted_object: - genes: - - Not mentioned - exposures: - - None mentioned - gene_exposures_relationships: - - molecular_activity: Not applicable - gene: Not applicable -input_text: |- - Title: 3D printed infliximab suppositories for rectal biologic delivery. - Abstract: Infliximab is a monoclonal antibody that plays an important role in the management and treatment of chronic inflammatory bowel diseases (IBD). Due to its macromolecular structure, its delivery through the oral route is challenging, limiting its administration to only via the parenteral route. The rectal route offers an alternative way for administering infliximab, allowing it to be localised at the disease site and circumventing its passage across the alimentary canal and thus, maintaining its integrity and bioactivity. Three-dimensional (3D) printing is an advanced production technology that permits the creation of dose-flexible drug products from digital designs. The current study assessed the feasibility of utilising semi-solid extrusion 3D printing for the fabrication of infliximab-loaded suppositories for the local treatment of IBD. Various printing inks composed of Gelucire® (48/16 or 44/14) mixed with coconut oil and/or purified water were investigated. It was shown that following reconstitution in water, the infliximab solution can be directly incorporated into the printing ink of Gelucire® 48/16 and can withstand the extrusion process, resulting in well-defined suppositories. Since water content and temperature are critical for safeguarding infliximab's potency, the effect of changing the composition of the printing inks and printing parameters on infliximab's biologic efficiency was evaluated by measuring its binding capacity (i.e., the amount of infliximab that actively binds to its antigen to exert an effect). Despite drug loading assays showing that infliximab remains intact following printing, it was found that the incorporation of water in isolation results in only ∼65% binding capacity. However, when oil is added to the mixture, infliximab's binding capacity increases up to ∼85%. These promising results demonstrate that 3D printing has the potential to be exploited as a novel platform for fabricating dosage forms containing biopharmaceuticals, avoiding patients' compliance issues observed with injectables and addressing their unmet needs.© 2023 The Authors. - Keywords: Biologicals and monoclonal antibodies; Digital medicine production; Extrusion-assisted additve manufacturing of a suppository formulation; Pressure-assisted syringe; Rectal drug delivery; Tumour necrosis factor-alpha (TNF-alpha) inhibitors; Ulcerative colitis (UC) and Crohn's disease (CD) -raw_completion_output: |- - genes: None mentioned in the text - exposures: infliximab - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - infliximab - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Serum amyloid A and metabolic disease: evidence for a critical role in chronic inflammatory conditions. - Abstract: Serum amyloid A (SAA) subtypes 1-3 are well-described acute phase reactants that are elevated in acute inflammatory conditions such as infection, tissue injury, and trauma, while SAA4 is constitutively expressed. SAA subtypes also have been implicated as playing roles in chronic metabolic diseases including obesity, diabetes, and cardiovascular disease, and possibly in autoimmune diseases such as systemic lupus erythematosis, rheumatoid arthritis, and inflammatory bowel disease. Distinctions between the expression kinetics of SAA in acute inflammatory responses and chronic disease states suggest the potential for differentiating SAA functions. Although circulating SAA levels can rise up to 1,000-fold during an acute inflammatory event, elevations are more modest (∼5-fold) in chronic metabolic conditions. The majority of acute-phase SAA derives from the liver, while in chronic inflammatory conditions SAA also derives from adipose tissue, the intestine, and elsewhere. In this review, roles for SAA subtypes in chronic metabolic disease states are contrasted to current knowledge about acute phase SAA. Investigations show distinct differences between SAA expression and function in human and animal models of metabolic disease, as well as sexual dimorphism of SAA subtype responses.© 2023 den Hartigh, May, Zhang, Chait and Blaser. - Keywords: SAA; adipocytes, macrophages; cardiovascular disease; diabetes; intestine; liver; obesity -raw_completion_output: |- - genes: SAA - - exposures: not mentioned - - gene_exposures_relationships: not mentioned -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - not mentioned - - === - -extracted_object: - genes: - - SAA - exposures: - - not mentioned - gene_exposures_relationships: - - molecular_activity: not mentioned - gene: not mentioned -input_text: |- - Title: Probiotic lactic acid bacteria alleviate pediatric IBD and remodel gut microbiota by modulating macrophage polarization and suppressing epithelial apoptosis. - Abstract: The incidence of pediatric inflammatory bowel disease (PIBD) continues to rise. It was reported that the probiotic lactic acid bacteria Pediococcus pentosaceus (P. pentosaceus) can interfere with intestinal immunity, but it is still unknown whether it can alleviate PIBD and the concrete mechanism of immune regulation is unclear.For this study, 3-week-old juvenile mice were selected for modeling the development of PIBD. The mice treated with 2% DSS were randomly divided into two groups, which were given P. pentosaceus CECT8330 and equal amounts of solvent, respectively. The feces and intestinal tissue were collected for the mechanism exploration in vivo. THP-1 and NCM460 cells were used to investigate the effects of P. pentosaceus CECT8330 on macrophage polarization, epithelial cell apoptosis, and their crosstalk in vitro.P. pentosaceus CECT8330 obviously alleviated colitis symptoms of juvenile mice, including weight loss, colon length shortening, spleen swelling, and intestinal barrier function. Mechanistically, P. pentosaceus CECT8330 could inhibit intestinal epithelial apoptosis by suppressing the NF-κB signaling pathway. Meanwhile, it reprogramed macrophages from a pro-inflammatory M1 phenotype to an anti-inflammatory M2 phenotype, leading to a decreased secretion of IL-1β which contributes to the reduction in ROS production and epithelial apoptosis. Additionally, the 16S rRNA sequence analysis revealed that P. pentosaceus CECT8330 could recover the balance of gut microbiota, and a significantly increased content of Akkermansia muciniphila was particularly observed.P. pentosaceus CECT8330 shifts macrophage polarization toward an anti-inflammatory M2 phenotype. The decreased production of IL-1β leads to a reduction in ROS, NF-κB activation, and apoptosis in the intestinal epithelium, all of which help to repair the intestinal barrier and adjust gut microbiota in juvenile colitis mice.Copyright © 2023 Hua, Pan, Chen, Jing, Xie, Gao, Huang, Chen, Gao, Xu and Li. - Keywords: Akkermansia muciniphila; Pediococcus pentosaceus CECT8330; intestinal epithelium apoptosis; macrophage polarization; pediatric IBD -raw_completion_output: |- - genes: NF-κB - exposures: Pediococcus pentosaceus CECT8330; IL-1β; ROS - gene_exposures_relationships: NF-κB and Pediococcus pentosaceus CECT8330; IL-1β and ROS -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - IL-1β and ROS - - === - -extracted_object: - genes: - - NF-κB - exposures: - - Pediococcus pentosaceus CECT8330 - - IL-1β - - CHEBI:26523 - gene_exposures_relationships: - - molecular_activity: undeclared - gene: Pediococcus pentosaceus CECT8330 - - molecular_activity: IL-1β - gene: HGNC:1455 -named_entities: - - id: CHEBI:26523 - label: ROS - - id: HGNC:1455 - label: ROS -input_text: |- - Title: Comparison of the gut virus communities between patients with Crohn's disease and healthy individuals. - Abstract: The escalating incidence of Crohn's disease (CD), a debilitating ailment that ravages individuals and their families, has become a formidable issue over recent decades.In this study, fecal samples from patients with CD and healthy individuals were investigated by means of viral metagenomics.The fecal virome was analyzed and some suspected disease-causing viruses were described. A polyomavirus named HuPyV with 5,120 base pairs (bp) was found in the disease group. In a preliminary analysis employing large T region-specific primers, it was found that HuPyV was present in 3.2% (1/31) of healthy samples and 43.2% (16/37) of disease samples. Additionally, two other viruses from the anellovirus and CRESS-DNA virus families were found in fecal samples from CD patients. The complete genome sequences of these two viruses were described respectively, and the phylogenetic trees have been built using the anticipated amino acid sequences of the viral proteins.Further research is required to elucidate the relationship between these viruses and the onset and development of Crohn's disease.Copyright © 2023 Ding, Wan, Li, Ma, Zhang and Xu. - Keywords: CRESS-DNA virus; Crohn’s disease; anellovirus; inflammatory bowel disease; polyomavirus; viral metagenomics method -raw_completion_output: |- - genes: HuPyV - exposures: CRESS-DNA virus, anellovirus - gene_exposures_relationships: HuPyV - viral metagenomics method; CRESS-DNA virus - fecal samples from CD patients; anellovirus - fecal samples from CD patients -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - anellovirus - fecal samples from CD patients - - === - -extracted_object: - genes: - - HuPyV - exposures: - - CRESS-DNA virus, anellovirus - gene_exposures_relationships: - - molecular_activity: viral metagenomics method - gene: HuPyV - - molecular_activity: CRESS-DNA virus - gene: fecal samples from CD patients - - molecular_activity: exposure to anellovirus - gene: fecal samples -input_text: |- - Title: Combination therapy is not associated with improved rates of clinical or endoscopic remission in patients with inflammatory bowel disease treated with ustekinumab or vedolizumab: a retrospective study. - Abstract: Management of inflammatory bowel disease (IBD) involves biological agents, often in combination with thiopurines or methotrexate. The aim of our study was to compare clinical and endoscopic outcomes in IBD patients treated with vedolizumab or ustekinumab, as monotherapy or in combination with thiopurines or methotrexate.We conducted a retrospective cohort study of all patients aged ≥18 years with a diagnosis of ulcerative colitis or Crohn's disease, commenced on vedolizumab or ustekinumab between October 2015 and March 2022. Primary outcome was clinical remission or response calculated by partial Mayo score (remission: <3; response: improvement >1) for ulcerative colitis or Harvey-Bradshaw index (<5, >2 respectively) for Crohn's disease over 1 year. Secondary endpoints were treatment failure, relapse, endoscopic remission at 1 year. Statistical analysis was done using 2-sample Student's t and chi-square tests.A total of 159 IBD patients were included in the study, 85 (53%) on vedolizumab and 74 (47%) on ustekinumab. For those on vedolizumab, 61 (72%) patients had ulcerative colitis, and 24 (28%) has Crohn's disease. All patients on ustekinumab had Crohn's disease. Mean disease duration in was 9.4 and 13.5 years respectively. There was no difference in clinical response or remission for vedolizumab or ustekinumab monotherapy compared to combination therapy at 1 year. There was also no difference in treatment failure, relapse or endoscopic remission.Combining vedolizumab or ustekinumab with an immunomodulator is not superior to monotherapy in terms of clinical response or endoscopic remission up to 1 year in IBD.Copyright: © Hellenic Society of Gastroenterology. - Keywords: Crohn’s disease; Ulcerative colitis; biologics; thiopurines -raw_completion_output: |- - genes: None mentioned in the text - exposures: vedolizumab, ustekinumab, thiopurines, methotrexate - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - vedolizumab, ustekinumab, thiopurines, methotrexate - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Association of serum IgG4 and disease outcomes in patients with inflammatory bowel disease. - Abstract: The etiology of inflammatory bowel disease (IBD) is multifactorial and thought to be influenced by inappropriate activation of the gut mucosal immune system. As the only immunoglobulin G (IgG) subclass unable to activate the classical complement cascade, the role of IgG4 in IBD pathophysiology as an immunomodulator is controversial. This study aimed to determine the association of low, normal and high IgG4 levels with the outcomes of IBD patients.This was a retrospective study of a multisite tertiary care center database evaluating patients with IBD who had an IgG4 level drawn between 2014 and 2021. Subjects were divided into low, normal, and high IgG4 level groups for evaluation of demographic and clinical indicators of IBD activity and severity.Of 284 patients with IBD, 22 had low (7.7%), 16 high (5.6%), and 246 (86.6%) normal IgG4 levels. There was no difference in IBD subtype, mean age, age at IBD diagnosis, or smoking between the 3 groups. There was no difference in number of hospitalizations (P=0.20), C-reactive protein levels, need for intestinal resection (P=0.85), or presence of primary sclerosing cholangitis (P=0.15), pancreatitis (P=0.70), or perianal disease (P=0.68) between the groups. Significantly more patients in the low IgG4 group had previous exposure to vedolizumab compared to the other groups and more patients in the low IgG4 group received vedolizumab (P=0.04), azathioprine (P=0.04) and prednisone (P=0.03) during the 5-year follow up.In this study, a low serum IgG4 level was associated with higher rates of vedolizumab, azathioprine, and steroid use.Copyright: © Hellenic Society of Gastroenterology. - Keywords: IgG4; disease outcomes; disease severity; inflammatory bowel disease -raw_completion_output: |- - genes: None - exposures: IgG4, vedolizumab, azathioprine, prednisone - gene_exposures_relationships: None -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None - - === - -extracted_object: - genes: - - None - exposures: - - IgG4, vedolizumab, azathioprine, prednisone - gene_exposures_relationships: - - molecular_activity: None - gene: None -input_text: |- - Title: Alexithymic characteristics and interoceptive abilities are associated with disease severity and levels of C-reactive protein and cytokines in patients with inflammatory bowel disease. - Abstract: Alexithymia and atypical gut-brain signaling have been linked to the pathophysiology of inflammatory bowel disease (IBD). We herein assessed IBD patients' alexithymia levels and interoceptive abilities, and detected potential correlations with psychological distress, symptom severity and disease activity, and inflammation indices.Adult IBD outpatients and healthy controls were recruited. Alexithymia was assessed using the Toronto Alexithymia Scale, interoceptive accuracy using the Heartbeat Counting Test (cardiac interoception) and the Water Load Test-II (gastric interoception), and interoceptive sensibility using the Multidimensional Assessment of Interoceptive Awareness (MAIA).Forty-one patients with Crohn's disease (CD), 16 with ulcerative colitis (UC), and 50 healthy controls were included. In CD patients, the level of externally oriented thinking and total alexithymia score were correlated with disease activity (P=0.027 and P=0.047, respectively), while in UC patients difficulties in identifying emotions were linked to disease activity (P=0.007). In CD patients, the Noticing, Not-Worrying and Emotional Awareness MAIA subscale score were correlated with C-reactive protein levels (P=0.005, P=0.048 and P=0.005), the Noticing subscale score with interleukin (IL)-1β levels (r=-0.350, P=0.039), the Not-Distracting subscale score with IL-6 levels (r=-0.402, P=0.017), and the Emotional Awareness subscale score with IL-1β (r=-0.367, P=0.030) and IL-6 (r=-0.379, P=0.025) levels. Finally, in UC patients, the Not-Worrying subscale score was significantly associated with IL-6 levels (r=-0.532, P=0.049), while difficulties in identifying emotions were linked to IL-8 levels (r=0.604, P=0.022).Emotional and interoceptive processing is associated with IBD disease activity, suggesting a potential implication for IBD pathophysiology.Copyright: © Hellenic Society of Gastroenterology. - Keywords: Alexithymia; cytokines; inflammatory bowel disease; interoception -raw_completion_output: |- - genes: N/A - exposures: cytokines - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - cytokines - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: Cutaneous Crohn's disease after proctocolectomy for medically refractory colonic Crohn's disease: a case series and review of the literature. - Abstract: Cutaneous Crohn's disease (CCD), also known as metastatic Crohn's disease (CD), is one of the rarest and most challenging cutaneous manifestations of CD. It is characterized by non-caseating granulomatous inflammation of the skin at sites that are non-contiguous with the gastrointestinal (GI) tract. Diagnosis of CCD needs a high clinical suspicion since morphological presentation varies widely and lacks an apparent correlation to the activity of the luminal CD. The onset of CCD in patients without active GI CD is a particularly understudied phenomenon.We present a case series of a unique patient group who developed CCD while in remission from a luminal CD perspective, mainly after a proctocolectomy for Crohn's colitis. We also provide a literature review and summary of case reports of CCD after proctocolectomy.Our 4 adult patients diagnosed with CCD after proctocolectomy presented herein, were successfully treated with high-dose corticosteroids, followed by biologic therapy. Furthermore, a comprehensive review of CCD is provided regarding its pathogenesis, clinical presentation, differential diagnosis, and the evidence behind the available treatments.CCD should be considered in any CD patient presenting with skin lesions regardless of their disease activity status and history of proctocolectomy. The treatment remains challenging; biologics remain the cornerstone and a multidisciplinary approach is recommended. Larger randomized clinical trials are essential to determine the optimal treatment protocol and to improve outcomes.Copyright: © Hellenic Society of Gastroenterology. - Keywords: Cutaneous Crohn’s disease; dermatologic manifestations; inflammatory bowel disease; metastatic Crohn’s disease; proctocolectomy -raw_completion_output: |- - genes: None mentioned in the text. - exposures: high-dose corticosteroids, biologic therapy, proctocolectomy. - gene_exposures_relationships: None mentioned in the text. -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text. - - === - -extracted_object: - genes: - - None mentioned in the text. - exposures: - - high-dose corticosteroids, biologic therapy, proctocolectomy. - gene_exposures_relationships: - - molecular_activity: None mentioned in the text. - gene: None mentioned in the text. -input_text: |- - Title: Outcome of inflammatory bowel disease patients with prior malignancy. - Abstract: Inflammatory bowel disease (IBD) treatment options, such as anti-tumor necrosis factor (TNF) agents and thiopurines, are associated with an increased risk of certain malignancies. However, the management of IBD patients with prior malignancy is not well defined and the literature is scarce. The main aim of this study was to describe the outcome of IBD patients with prior malignancy, or malignancy before first exposure to IBD-related biologic or immunosuppressive treatment.The study cohort included adult IBD patients followed in a tertiary academic center, with at least one malignancy diagnosed before IBD diagnosis or before initiation of IBD-related treatment. The main outcome of interest was a relapse of the previous malignancy or development of a second malignancy.Our database included 1112 patients with both IBD and malignancy. Of these, 86 (9%) who had their malignancy diagnosed before IBD-related treatment initiation were identified, while 10/86 patients (9%) were further diagnosed with a second primary malignancy. Twenty patients, (20/86, 23%) had recurrence of a previous malignancy, most commonly non-melanoma skin cancer (NMSC), found in 9/20 patients (45%). Treatment with infliximab was found to be significantly associated with recurrence of NMSC (P=0.003).Anti-TNF treatment may be associated with an increased risk of NMSC recurrence. This underscores the importance of rigorous dermatological follow up in IBD patients with previous NMSC treated with anti-TNFs.Copyright: © Hellenic Society of Gastroenterology. - Keywords: Inflammatory bowel disease; malignancy; recurrent; secondary; therapy -raw_completion_output: |- - genes: TNF - exposures: anti-TNF agents, thiopurines, infliximab - gene_exposures_relationships: TNF - infliximab -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - TNF - infliximab - - === - -extracted_object: - genes: - - HGNC:11892 - exposures: - - anti-TNF agents, thiopurines, infliximab - gene_exposures_relationships: - - molecular_activity: infliximab - gene: HGNC:11892 -named_entities: - - id: HGNC:11892 - label: TNF -input_text: |- - Title: Knowledge mapping of COVID-19 and autoimmune diseases: a visual and bibliometric analysis. - Abstract: Many studies have shown an association between COVID-19 and autoimmune diseases (ADs). Studies on COVID-19 and ADs have also increased significantly, but there is no bibliometric analysis to summarize the association between COVID-19 and ADs. The purpose of this study was to perform a bibliometric and visual analysis of published studies related to COVID-19 and ADs.Based on the Web of Science Core Collection SCI-Expanded database, we utilize Excel 2019 and visualization analysis tools Co-Occurrence13.2 (COOC13.2), VOSviewer, CiteSpace, and HistCite for analysis.A total of 1736 related kinds of papers were included, and the number of papers presented an overall increasing trend. The country/region with the most publications is the USA, the institution is the Harvard Medical School, the author is Yehuda Shoenfeld from Israel, and the journal is Frontiers in Immunology. Research hotspots include immune responses (such as cytokines storm), multisystem ADs (such as systemic lupus erythematosus, rheumatoid arthritis, and multiple sclerosis), treatment modalities (such as hydroxychloroquine, rituximab), vaccination and autoimmune mechanisms (such as autoantibodies, molecular mimicry). The future research direction may be the mechanisms and treatment ideas of the association between ADs and COVID-19 (such as NF-κB, hyperinflammation, antiphospholipid antibodies, neutrophil extracellular traps, granulocyte-macrophage colony-stimulating factor), other cross-diseases of COVID-19 and ADs (such as inflammatory bowel disease, chronic mucocutaneous candidiasis, acute respiratory distress syndrome).The growth rate of publications regarding ADs and COVID-19 has risen sharply. Our research results can help researchers grasp the current status of ADs and COVID-19 research and find new research directions in the future.© 2023. The Author(s). - Keywords: Autoimmune diseases; COVID-19; Frontiers; Hotspots; Keywords analysis -raw_completion_output: |- - genes: NF-κB - exposures: hydroxychloroquine, rituximab - gene_exposures_relationships: NF-κB - hydroxychloroquine; NF-κB - rituximab -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - NF-κB - rituximab - - === - -extracted_object: - genes: - - NF-κB - exposures: - - hydroxychloroquine, rituximab - gene_exposures_relationships: - - molecular_activity: hydroxychloroquine - gene: NF-κB - - molecular_activity: NF-kB - gene: rituximab -input_text: |- - Title: Lymphogranuloma venereum and CMV co-infection mimicking ulcerative proctitis in a non-immunocompromised patient. - Abstract: - Keywords: -raw_completion_output: |- - genes: N/A - exposures: Lymphogranuloma venereum, CMV - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - Lymphogranuloma venereum, CMV - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: Mechanism by which oleracein E alleviates TNBS-induced ulcerative colitis. - Abstract: This study aimed to investigate the effect of oleracein E (OE) in improving 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced ulcerative colitis (UC).Lipopolysaccharide (LPS) was used to induce a UC cell model, and TNBS was used to induce a UC rat model. ELISA was performed to assess the levels of inflammatory factors (IL-1β, TNF-α, and IL-6). Moreover, the activities of catalase (CAT), myeloperoxidase (MPO), and malonaldehyde (MDA) were detected by kits. Western blotting was performed to assess related proteins of the Nrf2/HO-1 signaling pathway, tight junction protein (ZO-1, Occludin, and claudin-2) expression levels, and apoptosis-related proteins (Bcl2, Bax, and cleaved caspase 3). Flow cytometry was used to analyze ROS levels. The morphology of colon tissues and the apoptosis of cells were detected by HE and TUNEL staining, respectively.OE significantly increased the activity of CAT and decreased the activity of MPO in LPS-induced Caco-2 cells and TNBS-induced UC rats. However, the levels of IL-1β, IL-6, and TNF-α were markedly reduced both in vivo and in vitro. In addition, OE significantly increased the levels of Nrf2/HO-1 signaling pathway-related proteins and tight junction proteins and inhibited cell apoptosis. HE staining showed that OE significantly decreased the severity of acute TNBS-induced colitis in rats.OE may exert a regulatory effect on ameliorating intestinal barrier injury and reducing inflammation and oxidative stress levels by activating the Nrf2/HO-1 pathway.Copyright © 2023 The Author(s). Published by Wolters Kluwer Health, Inc. - Keywords: -raw_completion_output: |- - genes: Nrf2, HO-1, ZO-1, Occludin, claudin-2, Bcl2, Bax, cleaved caspase 3 - - exposures: oleracein E (OE), 2,4,6-trinitrobenzene sulfonic acid (TNBS), Lipopolysaccharide (LPS) - - gene_exposures_relationships: OE to Nrf2/HO-1 pathway -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - OE to Nrf2/HO-1 pathway - - === - -extracted_object: - genes: - - Nrf2, HO-1, ZO-1, Occludin, claudin-2, Bcl2, Bax, cleaved caspase 3 - exposures: - - CHEBI:48113 - gene_exposures_relationships: - - molecular_activity: OE to Nrf2/HO-1 pathway - gene: HGNC:4071 -named_entities: - - id: CHEBI:48113 - label: oleracein E (OE), 2,4,6-trinitrobenzene sulfonic acid (TNBS), Lipopolysaccharide - (LPS) - - id: HGNC:4071 - label: Nrf2 -input_text: |- - Title: Protective effect of Arum maculatum against dextran sulfate sodium induced colitis in rats. - Abstract: Ulcerative colitis (UC) is an inflammatory disease of the large intestine that is characterized by diarrhea, bloody stools, abdominal pain and mucosal ulceration. UC is treated with nonsteroidal anti-inflammatory drugs, corticosteroids or immunosuppressants, but long-term use of these drugs can cause adverse effects. Arum maculatum is used as a traditional treatment for digestive system disorders, but its use for treatment of UC has not been investigated rigorously. We investigated the possible protective effect of a methanol extract of A. maculatum against dextran sulfate sodium (DSS) induced experimental UC in rats. Total phenolic and flavonoid contents of the extract were 32.919 ± 1.125 mg gallic acid equivalent (GAE)/g and 52.045 ± 7.902 µg rutin equivalent (RE)/mg, respectively. The half-maximal inhibitory concentration (IC50) for the extract was 105.76 µg/ml according to the 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity assay. Effects of A. maculatum extract on UC induced by DSS were assessed both macroscopically and histologically. We also investigated effects of A. maculatum extract on malondialdehyde (MDA) levels and the oxidative stress index (OSI) in normal rats and rats with UC. We found that treatment with A. maculatum extract protected the colon against DSS induced UC in a dose-dependent manner. - Keywords: Arum maculatum; inflammatory bowel disease; medicinal plant; rats; ulcerative colitis -raw_completion_output: |- - genes: None mentioned in the text. - exposures: dextran sulfate sodium - gene_exposures_relationships: None mentioned in the text. -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text. - - === - -extracted_object: - genes: - - None mentioned in the text. - exposures: - - dextran sulfate sodium - gene_exposures_relationships: - - molecular_activity: None mentioned in the text. - gene: None mentioned in the text. -input_text: |- - Title: Reporting of endoscopy and histology of ulcerative colitis in routine clinical practice: How far we are! - Abstract: - Keywords: clinical practice; endoscopy; histology; inflammatory bowel disease; ulcerative colitis -raw_completion_output: |- - genes: - exposures: - gene_exposures_relationships: -prompt: |+ - From the text below, extract the following entities in the following format: - - genes: - exposures: - gene_exposures_relationships: - - - Text: - Title: Reporting of endoscopy and histology of ulcerative colitis in routine clinical practice: How far we are! - Abstract: - Keywords: clinical practice; endoscopy; histology; inflammatory bowel disease; ulcerative colitis - - === - -extracted_object: {} -input_text: |- - Title: Clinical features analysis of Kawasaki disease with abdominal symptoms as the first manifestation. - Abstract: To investigate the clinical characteristics of Kawasaki disease (KD) presenting with abdominal manifestation as the first manifestation. Our findings may help improve the cognition of KD with abdominal complications, and avoid misdiagnosis and missed diagnosis. A retrospective analysis was conducted of 1490 KD patients admitted to Shengjing Hospital between January 2019 and March 2022. Clinical characteristics, related factors, and prognosis of KD with abdominal manifestation as first manifestation were analyzed. Based on the presenting symptoms, patients were divided into gastrointestinal symptom group (n = 141), liver dysfunction group (n = 55), and control group (n = 1294). In the gastrointestinal group, diarrhea [100 cases (70.9%)], vomiting [55 cases (39.0%)], and abdominal pain [34 cases (24.1%)] were the most common symptoms at onset. 8 cases (5.7%) were complicated with pseudo-intestinal obstruction, 6 cases (4.3%) with ischemic colitis, 5 cases (3.5%) with pancreatitis, 2 cases (1.4%) with appendicitis, and 1 case (0.7%) with cholecystitis. Comparied to ordinary gastroenteritis caused by infection, gastroenteritis with KD has longer fever duration before treatment, higher WBC, PLT, CRP, AST levels and lower albumin levels. All patients in the liver dysfunction group had elevated transaminases, and 19 patients (34.5%) presented with jaundice. In the gastrointestinal group, the average hospital stay was 10.3 days, and the incidence of IVIG unresponsiveness and coronary artery lesion were 18.4% and 19.9%, respectively, which were significantly higher than that in the control group. In the liver dysfunction group, the average hospital stay (11.18 days), incidence of IVIG unresponsiveness (25.5%), and incidence of coronary artery lesion (29.1%) were significantly higher than that in the control group. On multivariate logistic regression analysis, gastrointestinal involvement, fever duration, ALT, PLT, and CRP were identified as risk factors for CAL, younger age, gastrointestinal involvement and fever duration were risk factors for IVIG unresponsiveness.  Conclusion: KD with gastrointestinal involvement is associated with a higher risk of IVIG unresponsiveness and coronary artery lesion. KD should be considered in the differential diagnosis of children with acute fever, especially those with gastrointestinal involvement and liver dysfunction. What is Known: • Fever duration, PLT, and CRP were identified as risk factors for CAL. Timely diagnosis and application of IVIG treatment can avoid exploratory laparotomy for ileus, appendectomy for misdiagnosed appendicitis, colonoscopy for misdiagnosed inflammatory bowel disease, and reduce the complications of CAL and IVIG unresponsiveness. What is New: • Abdominal symptoms as the first manifestation can be an independent risk factor for CAL and IVIG unresponsiveness. KD should be conside -raw_completion_output: |- - genes: None mentioned in the text. - exposures: infection, pseudointestinal obstruction, ischemic colitis, pancreatitis, appendicitis, cholecystitis, gastroenteritis, IVIG treatment, fever, ALT, CRP. - gene_exposures_relationships: None mentioned in the text. -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text. - - === - -extracted_object: - genes: - - None mentioned in the text. - exposures: - - infection, pseudointestinal obstruction, ischemic colitis, pancreatitis, appendicitis, - cholecystitis, gastroenteritis, IVIG treatment, fever, ALT, CRP. - gene_exposures_relationships: - - molecular_activity: None mentioned in the text. - gene: None mentioned in the text. -input_text: |- - Title: Decoding the microbiome: advances in genetic manipulation for gut bacteria. - Abstract: Studies of the gut microbiota have revealed associations between specific bacterial species or community compositions with health and disease, yet the causal mechanisms underlying microbiota gene-host interactions remain poorly understood. This is partly due to limited genetic manipulation (GM) tools for gut bacteria. Here, we review current advances and challenges in the development of GM approaches, including clustered regularly interspaced short palindromic repeats (CRISPR)-Cas and transposase-based systems in either model or non-model gut bacteria. By overcoming barriers to 'taming' the gut microbiome, GM tools allow molecular understanding of host-microbiome associations and accelerate microbiome engineering for clinical treatment of cancer and metabolic disorders. Finally, we provide perspectives on the future development of GM for gut microbiome species, where more effort should be placed on assembling a generalized GM pipeline to accelerate the application of groundbreaking GM tools in non-model gut bacteria towards both basic understanding and clinical translation.Copyright © 2023 Elsevier Ltd. All rights reserved. - Keywords: CRISPR-Cas; genetic manipulation tools; gut microbiome; host–microbe interactions; transposon -raw_completion_output: |- - genes: Not mentioned in the text. - - exposures: CRISPR-Cas, transposase-based systems - - gene_exposures_relationships: CRISPR-Cas to genetic manipulation tools; transposase-based systems to genetic manipulation tools -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - transposase-based systems to genetic manipulation tools - - === - -extracted_object: - genes: - - Not mentioned in the text. - exposures: - - CRISPR-Cas, transposase-based systems - gene_exposures_relationships: - - molecular_activity: genetic manipulation tools - gene: CRISPR-Cas - - molecular_activity: transposase-based systems - gene: genetic manipulation tools -input_text: |- - Title: Heterogeneity in protocols and outcomes to study the effect of renin-angiotensin system blockers in inflammatory bowel disease: A systematic review. - Abstract: The renin-angiotensin system (RAS) has been associated with inflammatory bowel disease (IBD), supporting translational relevance of RAS blockers. Comparability of study design/outcomes is fundamental for data analysis/discussion.We aimed at evaluating the heterogeneity among protocols and outcomes to study the effect of angiotensin-converting enzyme inhibitors or angiotensin receptor blockers in IBD.This study was performed and reported in accordance with the Cochrane recommendations and PRISMA (PROSPERO-CRD42022323853). Systematic searches were performed in PubMed, Scopus and Web of Science. Studies that met the inclusion criteria were selected. Quality assessment of the studies was done with the SYRCLES's risk of bias tools for animal studies.Thirty-five pre-clinical studies and six clinical studies were included. Chemical induction of colitis was the most used model, but variable doses of the induction agent were reported. All studies reported at least a disease activity index, a macroscopic score, or a histologic assessment, but these scores were methodologically heterogeneous and reported for different characteristics. Great heterogeneity was also found in drug interventions. Inflammatory markers assessed as outcomes were different across studies.Lack of standardization of protocols and outcomes among studies threatens the evidence on how RAS blockers influence IBD outcomes.© 2023 Société Française de Pharmacologie et de Thérapeutique. Published by John Wiley & Sons Ltd. - Keywords: angiotensin-converting enzyme; colitis; heterogeneity; inflammatory bowel disease; renin-angiotensin system blockers; variability -raw_completion_output: |- - genes: none mentioned in the text - - exposures: renin-angiotensin system blockers; angiotensin-converting enzyme inhibitors; angiotensin receptor blockers - - gene_exposures_relationships: none mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - none mentioned in the text - - === - -extracted_object: - genes: - - none mentioned in the text - exposures: - - renin-angiotensin system blockers - - CHEBI:35457 - - angiotensin receptor blockers - gene_exposures_relationships: - - molecular_activity: none mentioned in the text - gene: none mentioned in the text -named_entities: - - id: CHEBI:35457 - label: angiotensin-converting enzyme inhibitors -input_text: |- - Title: Antimicrobial therapies for chronic pain (part 2): the prevention and treatment of chronic pain. - Abstract: The discovery and development of antimicrobial therapies represents one of the most significant advancements in modern medicine. Although the primary therapeutic intent of antimicrobials is to eliminate their target pathogens, several antimicrobials have been shown to provide analgesia as a secondary benefit. Antimicrobials have demonstrated analgesic effects in conditions that involve dysbiosis or potential subclinical infection (e.g ., chronic low back pain with Modic type 1 changes; chronic prostatitis/chronic pelvic pain; irritable bowel syndrome; inflammatory bowel disease; functional gastrointestinal disorders/dyspepsia; myalgic encephalomyelitis/chronic fatigue syndrome), and might even prevent the chronification of pain after acute infections that are associated with excessive systemic inflammation (e.g ., post COVID-19 condition/long Covid, rheumatic fever). Clinical studies often assess the analgesic effects of antimicrobial therapies in an observational manner, without the ability to identify causative relationships, and significant gaps in the understanding remain regarding the analgesic potential of antimicrobials. Numerous interrelated patient-specific, antimicrobial-specific, and disease-specific factors altogether contribute to the perception and experience of pain, and each of these requires further study. Given worldwide concerns regarding antimicrobial resistance, antimicrobials must continue to be used judiciously and are unlikely to be repurposed as primary analgesic medications. However, when equipoise exists among several antimicrobial treatment options, the potential analgesic benefits of certain antimicrobial agents might be a valuable aspect to consider in clinical decision-making. This article (the second in a two-part series) aims to comprehensively review the evidence on the prevention and treatment of chronic pain using antimicrobial therapies and suggest a framework for future studies on this topic. - Keywords: Analgesia; Anti-Bacterial Agents; Anti-Infective Agents; Antiviral Agents; Central Nervous System Sensitization; Chronic Pain; Infections; Neuralgia; Nociceptive Pain; Pain Management -raw_completion_output: |- - genes: - - exposures: Antimicrobials, pathogens, dysbiosis, subclinical infection, excessive systemic inflammation, post COVID-19 condition/long Covid, rheumatic fever, antimicrobial resistance - - gene_exposures_relationships: Not mentioned in the text. -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Not mentioned in the text. - - === - -extracted_object: - exposures: - - Antimicrobials, pathogens, dysbiosis, subclinical infection, excessive systemic - inflammation, post COVID-19 condition/long Covid, rheumatic fever, antimicrobial - resistance - gene_exposures_relationships: - - molecular_activity: Not mentioned in the text. - gene: Not mentioned in the text. -input_text: |- - Title: Antimicrobial therapies for chronic pain (part 1): analgesic mechanisms. - Abstract: There is increasing evidence that the relationship between chronic pain and infections is complex and intertwined. Bacterial and viral infections can cause pain through numerous mechanisms such as direct tissue damage and inflammation, the induction of excessive immunologic activity, and the development of peripheral or central sensitization. Treating infections might relieve pain by attenuating these processes, but a growing body of literature suggests that some antimicrobial therapies confer analgesic effects, including for nociceptive and neuropathic pain symptoms, and affective components of pain. The analgesic mechanisms of antimicrobials are indirect, but might be conceptualized into two broad categories: 1) the reduction of the infectious burden and associated pro-inflammatory processes; and 2) the inhibition of signaling processes (e.g., enzymatic and cytokine activity) necessary for nociception and maladaptive neuroplastic changes via off-target effects (unintended binding sites). For the former, there is evidence that symptoms of chronic low back pain (when associated with Modic type 1 changes), irritable bowel syndrome, inflammatory bowel disease, chronic pelvic pain, and functional dyspepsia might be improved after antibiotic treatment, though significant questions remain regarding specific regimens and dose, and which subpopulations are most likely to benefit. For the latter, there is evidence that several antimicrobial classes and medications exert analgesic effects independent of their reduction of infectious burden, and these include cephalosporins, ribavirin, chloroquine derivatives, rapalogues, minocycline, dapsone, and piscidin-1. This article aims to comprehensively review the existing literature for antimicrobial agents that have demonstrated analgesic efficacy in preclinical or clinical studies. - Keywords: Analgesia; Anti-Bacterial Agents; Anti-Infective Agents; Antiviral Agents; Central Nervous System Sensitization; Chronic Pain; Infections; Neuralgia; Nociceptive Pain; Pain Management -raw_completion_output: |- - genes: - exposures: antimicrobial therapies - gene_exposures_relationships: antimicrobial therapies have analgesic effects; antimicrobial therapies reduce infectious burden and associated pro-inflammatory processes; antimicrobial therapies inhibit signaling processes necessary for nociception and maladaptive neuroplastic changes -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - antimicrobial therapies inhibit signaling processes necessary for nociception and maladaptive neuroplastic changes - - === - -extracted_object: - exposures: - - antimicrobial therapies - gene_exposures_relationships: - - molecular_activity: antimicrobial therapies - gene: analgesic effects - - molecular_activity: antimicrobial therapies - gene: N/A - - molecular_activity: inhibit signaling processes - gene: antimicrobial therapies -input_text: |- - Title: Spondyloarthritides. - Abstract: The spondyloarthritides are a diverse group of distinct yet interrelated disease processes with overlapping clinical features. They are ankylosing spondylitis, reactive arthritis, inflammatory bowel disease-associated arthritis, and psoriatic arthritis. Genetically, these disease processes have been linked by the presence of HLA-B27. They manifest with axial and peripheral symptoms, such as inflammatory back pain, enthesitis, oligoarthritis, and dactylitis. The onset of symptoms can begin before the age of 45; however, because of the wide range of signs and symptoms, diagnosis can be delayed, leading to unchecked inflammation, structural damage, and later, restriction in physical mobility.Copyright © 2022 Elsevier Inc. All rights reserved. - Keywords: Ankylosing spondylitis; Axial spondylitis; Inflammatory bowel disease–associated spondyloarthritis; Psoriatic arthritis; Reactive arthritis; Spondyloarthritides -raw_completion_output: |- - genes: HLA-B27 - exposures: Not mentioned in the provided text. - gene_exposures_relationships: Not applicable (N/A) as no specific gene-exposure relationships are mentioned in the text. -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - Not applicable (N/A) as no specific gene-exposure relationships are mentioned in the text. - - === - -extracted_object: - genes: - - HLA-B27 - exposures: - - Not mentioned in the provided text. - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: Combining ultrasound radiomics, complete blood count, and serum biochemical biomarkers for diagnosing intestinal disorders in cats using machine learning. - Abstract: This retrospective analytical observational cohort study aimed to model and predict the classification of feline intestinal diseases from segmentations of a transverse section from small intestine ultrasound (US) image, complete blood count (CBC), and serum biochemical profile data using a variety of machine-learning approaches. In 149 cats from three institutions, images were obtained from cats with biopsy-confirmed small cell epitheliotropic lymphoma (lymphoma), inflammatory bowel disease (IBD), no pathology ("healthy"), and other conditions (warrant a biopsy for further diagnosis). CBC, blood serum chemistry, small intestinal ultrasound, and small intestinal biopsy were obtained within a 2-week interval. CBC and serum biomarkers and radiomic features were combined for modeling. Four classification schemes were investigated: (1) normal versus abnormal; (2) warranting or not warranting a biopsy; (3) lymphoma, IBD, healthy, or other conditions; and (4) lymphoma, IBD, or other conditions. Two feature selection methods were used to identify the top 3, 5, 10, and 20 features, and six machine learning models were trained. The average (95% CI) performance of models for all combinations of features, numbers of features, and types of classifiers was 0.886 (0.871-0.912) for Model 1 (normal vs. abnormal), 0.751 (0.735-0.818) for Model 2 (biopsy vs. no biopsy), 0.504 (0.450-0.556) for Model 3 (lymphoma, IBD, healthy, or other), and 0.531 (0.426-0.589), for Model 4 (lymphoma, IBD, or other). Our findings suggest model accuracies above 0.85 can be achieved in Model 1 and 2, and that including CBC and biochemistry data with US radiomics data did not significantly improve accuracy in our models.© 2023 The Authors. Veterinary Radiology & Ultrasound published by Wiley Periodicals LLC on behalf of American College of Veterinary Radiology. - Keywords: artificial intelligence; feline; intestine; lymphoma -raw_completion_output: |- - genes: No genes mentioned in the text. - exposures: No exposures mentioned in the text. - gene_exposures_relationships: No gene-exposures relationships mentioned in the text. -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - No gene-exposures relationships mentioned in the text. - - === - -extracted_object: - genes: - - No genes mentioned in the text. - exposures: - - No exposures mentioned in the text. - gene_exposures_relationships: - - molecular_activity: No mention of gene-exposures relationships - gene: No mention of gene-exposures relationships -input_text: |- - Title: Increasing Dietary Nutrient Levels Modulates Colon Immune Adaptation and Alleviates Inflammation in the Epithelial Heterogeneous Nuclear Ribonucleoprotein I (Hnrnp I) Knockout Mice. - Abstract: Heterogeneous nuclear ribonucleoprotein I (HNRNP I) is an RNA-binding protein essential for neonatal immune adaptation by downregulating interleukin-1 receptor-associated kinase (IRAK1) in toll-like receptor (TLR)-mediated NF-κB signaling pathways. TLR-mediated NF-κB is associated with chronic inflammation, including the development of inflammatory bowel diseases. Therefore, dietary protein intake is one of the major concerns for individuals with inflammatory bowel diseases. The present study aims to investigate the effects of a protein-enriched diet on intestinal inflammation and immune responses in a mouse model with aberrant NF-κB signaling in the colon.A transgenic mouse model with intestinal-epithelial-cell (IEC) specific Hnrnp I knocked out was used to investigate the effects of protein intake on the immune system in the colon. A control diet (CON) and a nutrient-dense modified diet (MOD) were fed to both the wild-type (WT) and the knockout (KO) male mice for 14 weeks. Inflammatory markers and colonic immune responses were examined, with gene expression and protein expression levels analyzed. IEC-specific Hnrnp I knocked out mice had significantly increased expression of the active NF-κB subunit, P65, in their colons. There was a concomitant induction of mRNA expression of Il1β, Il6, Cxcl1, and Ccl2. The number of CD4+ T cells in the distal colon was also increased in the KO mice. The results confirmed that KO mice had pro-inflammatory responses with aberrant NF-κB signaling in the colon. Importantly, increased nutrient density in their diets attenuated colon inflammation by decreasing the expression of pro-inflammatory cytokines, reducing P65 translocation, downregulating IRAK1, and limiting the number of CD4+ T cells recruited in Hnrnp I KO mice colon.A diet with increased nutrient density relieved the inflammation induced by knockout of Hnrnp I, attributable partially to the reduced expression of inflammatory and immune-modulating cytokines in the mouse distal colon.Copyright © 2023. Published by Elsevier Inc. - Keywords: Hnrnp I; Inflammation; colon immunity; dietary protein -raw_completion_output: |- - genes: Hnrnp I, IRAK1, Il1β, Il6, Cxcl1, Ccl2 - exposures: dietary protein, nutrient-dense modified diet - gene_exposures_relationships: Hnrnp I - downregulates IRAK1; nutrient-dense modified diet - attenuated colon inflammation -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - nutrient-dense modified diet - attenuated colon inflammation - - === - -extracted_object: - genes: - - Hnrnp I, IRAK1, Il1β, Il6, Cxcl1, Ccl2 - exposures: - - dietary protein, nutrient-dense modified diet - gene_exposures_relationships: - - molecular_activity: downregulates - gene: Hnrnp I - - molecular_activity: attenuated colon inflammation - gene: nutrient-dense modified diet -input_text: |- - Title: Prior Authorizations Delay Therapy, Impact Decision Making, and Lead to Adverse Events in IBD: 2022 Provider Survey. - Abstract: - Keywords: Crohn’s disease; Prior authorization; biologics; inflammatory bowel disease; ulcerative colitis -raw_completion_output: |- - genes: None given in the text - exposures: biologics - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None given in the text - exposures: - - biologics - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: High Frequency of Deep Infiltrating Endometriosis in Patients with Inflammatory Bowel Disease: A Nested Case-Control Study. - Abstract: Inflammatory bowel disease (IBD) and endometriosis are chronic inflammatory diseases occurring in young women, sharing some clinical manifestations. In a multidisciplinary approach, we aimed to investigate symptoms, type, and site of pelvic endometriosis in IBD patients versus non-IBD controls with endometriosis.In a prospective nested case-control study, all female premenopausal IBD patients showing symptoms compatible with endometriosis were enrolled. Patients were referred to dedicated gynecologists for assessing pelvic endometriosis by transvaginal sonography (TVS). Each IBD patient with endometriosis (cases) was retrospectively matched for age (±5 years) and body mass index (±1) with 4 patients with endometriosis at TVS but no-IBD (controls). Data were expressed as median [range]; the Mann-Whitney or Student t and χ2 tests were used for comparisons.Endometriosis was diagnosed in 25 (71%) out of 35 IBD patients with compatible symptoms including 12 (52.6%) Crohn's disease and 13 (47.4%) ulcerative colitis patients. Dyspareunia and dyschezia were significantly more frequent in cases versus controls (25 [73.7%] vs. 26 [45.6%]; p = 0.03). At TVS, deep infiltrating endometriosis (DIE) and posterior adenomyosis were significantly more frequently observed in cases versus controls (25 [100%] vs. 80 [80%]; p = 0.03 and 19 [76%] vs. 48 [48%]; p = 0.02).Endometriosis was detected in two-thirds of IBD patients with compatible symptoms. The frequency of DIE and posterior adenomyosis was higher in IBD than in controls. A diagnosis of endometriosis, often mimicking IBD activity, should be considered in subgroups of female patients with IBD.© 2023 S. Karger AG, Basel. - Keywords: Deep infiltrating endometriosis; Endometriosis; Inflammatory bowel disease -raw_completion_output: |- - genes: None mentioned in the text - exposures: None mentioned in the text - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - None mentioned in the text - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Manifestation of acute appendicitis as known but paradox visceral side effect of ulcerative colitis anti-inflammatory therapy with januskinase-inhibitor Tofacitinib (Xeljanz™). - Abstract: The etiopathogenesis of accompanying inflammatory phenomena and consequences of immunomodulation constitute a challenging and innovative field in the medical treatment of patients with autoimmune diseases.Based on i) clinical management experience gained from this challenging clinical case and ii) selective references of reports published in the scientific medical literature, we present an unusual counterfactual scientific case report. A patient diagnosed with ulcerative colitis undergoing januskinase (JAK)-inhibitor therapy developed acuteappendicitis as an unusual complication or as a visceral side effect of immunosuppressive/anti-inflammatory therapy.Scientific case report.(case description): Medical history: A 52-year-old male presented with spasmodic pain in the right lower abdomen lasting for two days (no fever, no bowel movement changes (no stool irregularities), no vomiting).Steroid-resistant ulcerative colitis treated with immunosuppressive therapy (Adalimumab administered for 10 months [next generation anti-TNFα mAb], Vendolizumab for 9 months [α4β7 integrin antagonist], Tofacitinib for 6 months); fructose intolerance, no previous abdominal surgery; medication: XeljanzTM (Tofacitinib, 5 mg 2x1; JAK-inhibitor; PFIZER PHARMA GmbH, Berlin,Germany); MutaflorTM (1x1; Ardeypharm GmbH, Herdecke, Germany).Pressure pain in the right lower abdomen with local muscular defense (Mc-Burney's/Lanz's point positive), no peritonism, Psoas-muscle sign positive.Laboratory parameters: standard value of white blood cell count, CrP: 25 mg/l.-Transabdominal ultrasound revealed hypertrophic 'appendix vermiformis' with detectable target-phenomenon and surrounding fluid.Indication for laparoscopic exploration.Under perioperative single-shot antibiotic administration with UnacidTM, the patient underwent emergency laparoscopic appendectomy due to confirmed acute appendicitis with additional lavage and placement of local drainage.The postoperative phase was uneventful (sufficient analgetic therapy, removal of local drainage on the 2nd postoperative day). The patient was discharged four days after surgery. Histopathology confirmed ulcero-phlegmonous, acute purulent appendicitis with fibrinous purulent mesenteriolitis.Immunosuppressive therapy was continued.Based on the paradoxon of an acute inflammatory disease (acute appendicitis) seen in the case of a patient undergoing immunosuppressive/anti-inflammatory treatment using a JAK-Inhibitor for ulcerative colitis, we consider this case worthy of publication although this side effect has previously been described in patients with rheumatoid arthritis. This might be the manifestation of i) an immunomodulatory effect that reduced or at least altered mucosal defense, including an increased risk of opportunistic infections, presenti -raw_completion_output: |- - genes: januskinase (JAK) - exposures: Tofacitinib (Xeljanz™) - gene_exposures_relationships: januskinase (JAK) - Tofacitinib (Xeljanz™) -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - januskinase (JAK) - Tofacitinib (Xeljanz™) - - === - -extracted_object: - genes: - - januskinase (JAK) - exposures: - - Tofacitinib (Xeljanz™) - gene_exposures_relationships: - - molecular_activity: exposure to a chemical toxin - gene: JAK -input_text: |- - Title: Prevention of colitis-induced liver oxidative stress and inflammation in a transgenic mouse model with increased omega-3 polyunsaturated fatty acids. - Abstract: Inflammatory bowel disease (IBD) is an immune-mediated gut dysfunction, which might also be associated with an inflammatory phenotype in the liver. It is known that the nutritional intake of omega-3 polyunsaturated fatty acids (n-3 PUFA) is inversely correlated to the severity and occurrence of IBD. In order to investigate whether n-3 PUFA can also reduce liver inflammation and oxidative liver damage due to colon inflammation, we explored the dextran sulfate sodium (DSS)-induced colitis model in wild-type and fat-1 mice with endogenously increased n-3 PUFA tissue content. Besides confirming previous data of alleviated DSS-induced colitis in the fat-1 mouse model, the increase of n-3 PUFA also resulted in a significant reduction of liver inflammation and oxidative damage in colitis-affected fat-1 mice as compared to wild-type littermates. This was accompanied by a remarkable increase of established inflammation-dampening n-3 PUFA oxylipins, namely docosahexaenoic acid-derived 19,20-epoxydocosapentaenoic acid and eicosapentaenoic acid-derived 15-hydroxyeicosapentaenoic acid and 17,18-epoxyeicosatetraenoic acid. Taken together, these observations demonstrate a strong inverse correlation between the anti-inflammatory lipidome derived from n-3 PUFA and the colitis-triggered inflammatory changes in the liver by reducing oxidative liver stress.Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved. - Keywords: Colitis; Fat-1 mice; Liver inflammation; Liver oxidative stress; n-3 PUFA -raw_completion_output: |- - genes: No gene mentioned in the text. - - exposures: omega-3 polyunsaturated fatty acids (n-3 PUFA), dextran sulfate sodium (DSS) - - gene_exposures_relationships: No gene to molecular activity relationships mentioned in the text. -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - No gene to molecular activity relationships mentioned in the text. - - === - -extracted_object: - genes: - - No gene mentioned in the text. - exposures: - - omega-3 polyunsaturated fatty acids (n-3 PUFA), dextran sulfate sodium (DSS) -input_text: |- - Title: Borrelia Burgdorferi, a Root Cause of Inflammatory Bowel Disease: A Case Report of Successful Treatment and Remission. - Abstract: The Borrelia species is recognized to cause a myriad of non-specific symptoms among Lyme patients. It has also been documented in the literature to have the ability to incite autoimmune responses. Despite this, very few clinical cases have ever put together the autoimmune connection to such infections, including in Crohn's disease.A 14-year-old adolescent male with a previous diagnosis of Crohn's disease was discovered to have underlying Lyme disease caused by Borrelia burgdorferi infection. Identifying this as a potential cause of his autoimmune condition, an integrative medical approach was initiated, resulting in successful treatment and complete remission.Lyme disease should be recognized as a potential trigger of autoimmune conditions, especially Crohn's disease. This underlying cause is novel to the literature and may help many patients obtain the proper diagnosis so that curative treatment may be received. - Keywords: -raw_completion_output: |- - genes: Borrelia burgdorferi - - exposures: Lyme disease, Borrelia burgdorferi - - gene_exposures_relationships: Borrelia burgdorferi -> autoimmune responses -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Borrelia burgdorferi -> autoimmune responses - - === - -extracted_object: - genes: - - Borrelia burgdorferi - exposures: - - Lyme disease, Borrelia burgdorferi - gene_exposures_relationships: - - molecular_activity: autoimmune responses - gene: Borrelia burgdorferi -input_text: |- - Title: Clinical Features and Natural History of Paediatric Patients with Ulcerative Proctitis: A Multicentre Study from the Paediatric IBD Porto Group of ESPGHAN. - Abstract: Ulcerative proctitis (UP) is an uncommon presentation in paediatric patients with ulcerative colitis. We aimed to characterize the clinical features and natural history of UP in children, and identify predictors of poor outcomes.Retrospective study involving 37 sites affiliated with the IBD Porto Group of ESPGHAN. Data were collected from patients aged<18 years diagnosed with UP between 01/01/2016-31/12/2020.We identified 196 patients with UP (median age at diagnosis 14.6 [IQR 12.5-16.0] years), with a median follow-up of 2.7 (IQR 1.7-3.8) years. The most common presenting symptoms were bloody stools (95%), abdominal pain (61%) and diarrhea )47%). At diagnosis, the median paediatric ulcerative colitis activity index (PUCAI) score was 25 (IQR 20-35), but most patients exhibited moderate-severe endoscopic inflammation. By the end-of-induction, 5-aminosalicylic acid administration orally, topically or both resulted in clinical remission rates of 48%, 48% and 73%, respectively. The rates of treatment escalation to biologics at 1, 3 and 5 years were 10%, 22% and 43%, respectively. In multivariate analysis, the PUCAI score at diagnosis was significantly associated with initiation of systemic steroids, or biologics, and subsequent acute severe colitis events and IBD-associated admission, with a score≥35 providing increased risk for poor outcomes. By the end of follow-up, 3.1% of patients underwent colectomy. Patients with proximal disease progression (48%) had significantly higher rates of cecal patch at diagnosis and higher PUCAI score by end-of-induction, compared to those without progression.Paediatric patients with UP exhibit high rates of treatment escalation and proximal disease extension.© The Author(s) 2023. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation. All rights reserved. For permissions, please email: journals.permissions@oup.com. - Keywords: children; inflammatory bowel disease; proctitis; ulcerative colitis -raw_completion_output: |- - genes: None mentioned in the text - exposures: 5-aminosalicylic acid - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - 5-aminosalicylic acid - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Smoking and colorectal cancer in inflammatory bowel disease: Quantity matters? - Abstract: - Keywords: -raw_completion_output: |- - genes: - - exposures: smoking; - - gene_exposures_relationships: smoking and colorectal cancer; -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - smoking and colorectal cancer - - === - -extracted_object: - exposures: - - NCIT:C154329 - gene_exposures_relationships: - - molecular_activity: NCIT:C154329 - gene: colorectal cancer -named_entities: - - id: NCIT:C154329 - label: smoking -input_text: |- - Title: Recent developments on BMPs and their antagonists in inflammatory bowel diseases. - Abstract: Inflammatory bowel diseases (IBDs), including ulcerative colitis, and Crohn's disease, are intestinal disorders characterized by chronic relapsing inflammation. A large proportion of patients with IBD will progress to develop colitis-associated colorectal cancer due to the chronic intestinal inflammation. Biologic agents that target tumour necrosis factor-α, integrin α4β7, and interleukin (IL)12/23p40 have been more successful than conventional therapies in treating IBD. However, drug intolerance and loss of response are serious drawbacks of current biologics, necessitating the development of novel drugs that target specific pathways in IBD pathogenesis. One promising group of candidate molecules are bone morphogenetic proteins (BMPs), members of the TGF-β family involved in regulating morphogenesis, homeostasis, stemness, and inflammatory responses in the gastrointestinal tract. Also worth examining are BMP antagonists, major regulators of these proteins. Evidence has shown that BMPs (especially BMP4/6/7) and BMP antagonists (especially Gremlin1 and follistatin-like protein 1) play essential roles in IBD pathogenesis. In this review, we provide an updated overview on the involvement of BMPs and BMP antagonists in IBD pathogenesis and in regulating the fate of intestinal stem cells. We also described the expression patterns of BMPs and BMP antagonists along the intestinal crypt-villus axis. Lastly, we synthesized available research on negative regulators of BMP signalling. This review summarizes recent developments on BMPs and BMP antagonists in IBD pathogenesis, which provides novel insights into future therapeutic strategies.© 2023. The Author(s). - Keywords: -raw_completion_output: |- - genes: BMP4, BMP6, BMP7, Gremlin1, follistatin-like protein 1 - exposures: bone morphogenetic proteins (BMPs) - gene_exposures_relationships: BMP4/6/7 are BMPs involved in IBD pathogenesis; Gremlin1 and follistatin-like protein 1 are BMP antagonists -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Gremlin1 and follistatin-like protein 1 are BMP antagonists - - === - -extracted_object: - genes: - - BMP4, BMP6, BMP7, Gremlin1, follistatin-like protein 1 - exposures: - - bone morphogenetic proteins (BMPs) - gene_exposures_relationships: - - molecular_activity: BMPs involved in IBD pathogenesis - gene: BMP4/6/7 - - molecular_activity: BMP antagonists - gene: Gremlin1 and follistatin-like protein 1 -input_text: |- - Title: 7TSG6 hyaluronan matrix remodeling dampens the inflammatory response during colitis. - Abstract: In response to tissue injury, changes in the extracellular matrix (ECM) can directly affect the inflammatory response and contribute to disease progression or resolution. During inflammation, the glycosaminoglycan hyaluronan (HA) becomes modified by tumor necrosis factor stimulated gene-6 (TSG6). TSG6 covalently transfers heavy chain (HC) proteins from inter-α-trypsin inhibitor (IαI) to HA in a transesterification reaction and is to date is the only known HC-transferase. By modifying the HA matrix, TSG6 generates HC:HA complexes that are implicated in mediating both protective and pathological responses. Inflammatory bowel disease (IBD) is a lifelong chronic disorder with well-described remodeling of the ECM and increased mononuclear leukocyte influx into the intestinal mucosa. Deposition of HC:HA matrices is an early event in inflamed gut tissue that precedes and promotes leukocyte infiltration. However, the mechanisms by which TSG6 contributes to intestinal inflammation are not well understood. The aim of our study was to understand how the TSG6 and its enzymatic activity contributes to the inflammatory response in colitis. Our findings indicate that inflamed tissues of IBD patients show an elevated level of TSG6 and increased HC deposition and that levels of HA strongly associate with TSG6 levels in patient colon tissue specimens. Additionally, we observed that mice lacking TSG6 are more vulnerable to acute colitis and exhibit an aggravated macrophage-associated mucosal immune response characterized by elevated pro-inflammatory cytokines and chemokines and diminished anti-inflammatory mediators including IL-10. Surprisingly, along with significantly increased levels of inflammation in the absence of TSG6, tissue HA levels in mice were found to be significantly reduced and disorganized, absent of typical "HA-cable" structures. Inhibition of TSG6 HC-transferase activity leads to a loss of cell surface HA and leukocyte adhesion, indicating that the enzymatic functions of TSG6 are a major contributor to stability of the HA ECM during inflammation. Finally, using biochemically generated HC:HA matrices derived by TSG6, we show that HC:HA complexes can attenuate the inflammatory response of activated monocytes. In conclusion, our data suggests that TSG6 exerts a tissue-protective, anti-inflammatory effect via the generation of HC:HA complexes that become dysregulated in IBD.Copyright © 2023. Published by Elsevier B.V. - Keywords: Colitis; Extracellular matrix; Hyaluronan; IBD; TSG6 -raw_completion_output: |- - genes: TSG6, IL-10 - exposures: tumor necrosis factor, inter-α-trypsin inhibitor, hyaluronan - gene_exposures_relationships: TSG6 with tumor necrosis factor, TSG6 with inter-α-trypsin inhibitor, TSG6 with hyaluronan -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - TSG6 with tumor necrosis factor, TSG6 with inter-α-trypsin inhibitor, TSG6 with hyaluronan - - === - -extracted_object: - genes: - - TSG6, IL-10 - exposures: - - tumor necrosis factor, inter-α-trypsin inhibitor, hyaluronan - gene_exposures_relationships: - - molecular_activity: hyaluronan - gene: HGNC:11898 -named_entities: - - id: HGNC:11898 - label: TSG6 -input_text: |- - Title: Delayed Ustekinumab Responders in Ulcerative Colitis Have Greater Inflammatory Burden but Similar Outcomes as Early Responders. - Abstract: Differences in one-year outcomes among early compared to delayed responders to vedolizumab have been demonstrated in ulcerative colitis. However, it is unclear whether similar differences exist with ustekinumab, and what factors differentiate delayed responders from non-responders.This was a post-hoc analysis of patient-level data from the UNIFI clinical trial. Ustekinumab-treated patients with clinical response, defined as reduction in total Mayo score ≥30% and ≥3 points from baseline with reduction in rectal bleeding subscore (RBS)≥1 or RBS≤1, at week 8 were deemed early responders and their outcomes were compared with delayed responders (week 8 non-responders who subsequently responded at week 16). The primary outcome assessed was one-year clinical remission (CR), defined as total Mayo score ≤2 and no subscore >1.We included 642 ustekinumab-treated patients, including 321 (50%) early responders, 115 (17.9%) delayed responders, and 205 (32.1%) non-responders. No differences were observed for one-year CR among early vs. delayed responders [132/321 (41.1%) vs. 40/115 (34.8%), p=0.233], nor for other outcomes assessed regardless of induction dose. Compared to early responders, delayed responders had more severe baseline Mayo endoscopic disease [88/115 (76.5%) vs. 206/321 (64.2%), p=0.015] and abnormal baseline CRP >3mg/L [83/115 (72.2%) vs. 183/321 (57%), p=0.004]. Compared to non-responders, delayed responders had a significant decline in CRP (F(4, 844), p<0.0001) and fecal calprotectin (F(4, 818), p<0.0001) through week 16.Compared with early ustekinumab responders, delayed responders had greater inflammatory burden at baseline. Early and delayed responders have similar one-year outcomes. Biomarker decline observed in delayed responders can help differentiate them from non-responders.Copyright © 2023 AGA Institute. Published by Elsevier Inc. All rights reserved. - Keywords: Endoscopic Improvement; Inflammatory Bowel Disease; Ulcerative Colitis -raw_completion_output: |- - genes: N/A - exposures: ustekinumab, vedolizumab - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - ustekinumab, vedolizumab - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: Eriocalyxin B ameliorated Crohn's disease-like colitis by restricting M1 macrophage polarization through JAK2/STAT1 signalling. - Abstract: M1 polarization of macrophages in the intestine is an important maintenance factor of the inflammatory response in Crohn's disease (CD). Eriocalyxin B (EriB) is a natural medicine that antagonizes inflammation. Our study aimed to determine the effects of EriB on CD-like colitis in mice, as well as the possible mechanism.2,4,6-trinitrobenzene sulfonic acid (TNBS) mice and Il-10-/- mice were used as CD animal models, and the therapeutic effect of EriB on CD-like colitis in mice was addressed by the disease activity index (DAI) score, weight change, histological analysis and flow cytometry assay. To assess the direct role of EriB in regulating macrophage polarization, bone marrow-derived macrophages (BMDMs) were induced to M1 or M2 polarization separately. Molecular docking simulations and blocking experiments were performed to explore the potential mechanisms by which EriB regulates the macrophage polarization.EriB treatment reduced body weight loss, DAI score and histological score, demonstrating the improvement of colitis symptoms in mice. In vivo and in vitro experiments both showed that EriB decreased the M1 polarization of macrophages, and suppressed the release of proinflammatory cytokines (IL-1β, TNF-α and IL-6) in mouse colons and BMDMs. The activation of Janus kinase 2/signal transducer and activator of transcription 1 (JAK2/STAT1) signals could be inhibited by EriB, which may be related to the regulation of EriB on M1 polarization.EriB inhibits the M1 polarization of macrophages by attenuating the JAK2/STAT1 pathway, which partially explains the potential mechanism by which EriB ameliorates colitis in mice, and provides a new regimen for the clinical treatment of CD.Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved. - Keywords: Colitis; Crohn's disease; Eriocalyxin B; JAK2/STAT1; macrophage -raw_completion_output: |- - genes: JAK2, STAT1 - exposures: Eriocalyxin B, 2,4,6-trinitrobenzene sulfonic acid (TNBS), IL-1β, TNF-α, IL-6 - gene_exposures_relationships: JAK2/STAT1 to Eriocalyxin B -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - JAK2/STAT1 to Eriocalyxin B - - === - -extracted_object: - genes: - - JAK2, STAT1 - exposures: - - CHEBI:48113 - gene_exposures_relationships: - - molecular_activity: JAK2/STAT1 - gene: Eriocalyxin B -named_entities: - - id: CHEBI:48113 - label: Eriocalyxin B, 2,4,6-trinitrobenzene sulfonic acid (TNBS), IL-1β, TNF-α, - IL-6 -input_text: |- - Title: Lack of Seroconversion Following COVID-19 Vaccination Is an Independent Risk Factor for SARS-CoV-2 Infection in Patients With Inflammatory Bowel Disease: Data from ESCAPE-IBD, an IG-IBD Study. - Abstract: - Keywords: SARS-CoV-2; Seroconversion; biologics; vaccine -raw_completion_output: |- - genes: none mentioned in the text - - exposures: SARS-CoV-2, biologics, vaccine - - gene_exposures_relationships: none mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - none mentioned in the text - - === - -extracted_object: - genes: - - none mentioned in the text - exposures: - - SARS-CoV-2, biologics, vaccine - gene_exposures_relationships: - - molecular_activity: none mentioned in the text - gene: none mentioned in the text -input_text: |- - Title: Neutrophil-only histological assessment of ulcerative colitis correlates with endoscopic activity and predicts long-term outcomes in a multicenter study. - Abstract: Absence of neutrophils is the minimum standard to consider histological remission of ulcerative colitis (UC). The PICaSSO Histological remission Index (PHRI) is a new simple index for UC based only on the detection of neutrophils. We evaluate PHRI's correlation with endoscopy and its prognostic value compared to other established indices.Consecutive patients with UC underwent colonoscopy at 2 referral centres (Birmingham, UK and Milan, Italy) and were followed up for 2 years. Correlation between histology (PHRI, Nancy [NHI] and Robarts [RHI]) and endoscopy (Mayo Endoscopic Score [MES]; Ulcerative Colitis Severity Endoscopic Index of Severity [UCEIS], and PICaSSO score) was calculated as Spearman coefficients. Diagnostic performance of endoscopy was assessed with ROC curves and outcome stratification with Kaplan-meier curves.192 patients with UC were enrolled, representing all grades of endoscopic severity. Correlation between histology and endoscopy did not differ significantly when using PHRI instead of NHI or RHI. In particular, PHRI's correlation with MES, UCEIS and PICaSSO was 0.745, 0.718, and 0.694, respectively. Endoscopically-assessed remission reflected the absence of neutrophils (PHRI = 0) with areas under the ROC curve of 0.905, 0.906, and 0.877 for MES, UCEIS, and PICaSSO, respectively. The hazard ratio for disease flare between patients in histological activity/remission was statistically similar (p>0.05) across indexes (2.752, 2.706, and 2.871 for RHI, NHI, and PHRI, respectively).PHRI correlates with endoscopy and stratifies risk of relapse similarly to RHI and NHI. Neutrophil-only assessment of UC is a simple yet viable alternative to established histological scores.© The Author(s) 2023. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation. All rights reserved. For permissions, please email: journals.permissions@oup.com. - Keywords: PHRI; PICaSSO; endoscopic remission; histological remission; inflammatory bowel diseases; neutrophils -raw_completion_output: |- - genes: None mentioned - exposures: PICaSSO, Nancy, Robarts, Mayo Endoscopic Score, Ulcerative Colitis Severity Endoscopic Index of Severity, PICaSSO score, RHI, NHI - gene_exposures_relationships: PHRI correlates with MES, UCEIS, PICaSSO; RHI, NHI, and PHRI reflect histological activity/remission; endoscopically-assessed remission reflects the absence of neutrophils (PHRI = 0) -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - endoscopically-assessed remission reflects the absence of neutrophils (PHRI = 0) - - === - -extracted_object: - genes: - - None mentioned - exposures: - - PICaSSO, Nancy, Robarts, Mayo Endoscopic Score, Ulcerative Colitis Severity - Endoscopic Index of Severity, PICaSSO score, RHI, NHI - gene_exposures_relationships: - - molecular_activity: PHRI - gene: PICaSSO - - molecular_activity: histological activity/remission - gene: RHI - - molecular_activity: exposure to a chemical toxin - gene: PHRI -input_text: |- - Title: Effect of Bariatric Surgery on Disease Outcomes in Patients with Inflammatory Bowel Disease: A US-based Propensity Matched Cohort Study. - Abstract: A growing body of evidence suggests a negative impact of obesity on the disease activity of inflammatory bowel disease (IBD). The primary aim of the study was to evaluate disease outcomes of IBD in patients after bariatric surgery (BS).Patients with IBD and morbid obesity who underwent BS were compared with patients with IBD and morbid obesity without BS in a retrospective, propensity-score matched cohort study using TriNetX, a multi-institutional database. The primary aim was to assess the 2-year risk of a composite of disease-related complications, which included intravenous steroid use or IBD-related surgery. Risk was expressed as adjusted odds ratios (aOR) with 95% confidence intervals (CI).In all, 482 patients (3.4%) with IBD and morbid obesity underwent BS (mean age 46.9±11.2 y old, mean BMI 42.1±7.72 kg/m2, Crohn's disease 60%). After propensity-score matching, the BS cohort had a lower risk (aOR 0.31, 95% CI 0.17-0.56) of a composite of IBD-related complications compared with the control cohort. After propensity-score matching, the BS cohort with sleeve gastrectomy had a decreased risk (aOR 0.45, 95% CI 0.31-0.66) of a composite of IBD-related complications. There was no difference in the risk (aOR 0.77, 95% CI 0.45-1.31) of a composite of IBD-related complications between the BS cohort with Roux-en-Y gastric bypass (RYGB) compared with the control cohort.Sleeve gastrectomy but not Roux-en-Y gastric bypass is associated with improved disease-specific outcomes in patients with IBD and morbid obesity.Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved. - Keywords: -raw_completion_output: |- - genes: N/A - exposures: Bariatric surgery - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - Bariatric surgery - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: The Effect of Renin-Angiotensin-Aldosterone System Blocking Agents on the Long-term Disease Course of Patients With Crohn's Disease. - Abstract: The renin-angiotensin-aldosterone system (RAAS) has been associated with gastrointestinal inflammation and fibrosis, suggesting that RAAS blockade may be beneficial in patients with inflammatory bowel disease. Using retrospective analysis, we aimed to compare the disease course of patients with Crohn's disease (CD) taking two commonly prescribed classes of RAAS-blocking agents.Patients with CD initiated on an angiotensin-converting enzyme inhibitor (ACEI) or angiotensin receptor blocker (ARB) between 2000 and 2016 were enrolled. Data on clinical, radiologic, and procedural surrogate markers of inflammatory bowel disease were collected in the subsequent 3, 5, and 10 years and compared with matched controls using univariate and multivariate analyses.Compared with controls, patients taking ARBs had fewer instances of corticosteroid use (1.06 vs 2.88, P < 0.01) at 10 years. Patients taking ACEIs had an overall worse disease course, with more imaging studies (3.00 vs 1.75, P = 0.03) and endoscopic procedures (2.70 vs 1.78, P = 0.01) at 5 years, and more imaging studies (6.19 vs 3.50, P < 0.01), endoscopic procedures (5.91 vs 3.78, P < 0.01), and gastrointestinal operations (0.59 vs 0.18, P < 0.02) at 10 years. Results remained significant on multivariate analysis, adjusting for CD characteristics and the use of other antihypertensive medications.Our study provides insight into the long-term use of RAAS-blocking agents in patients with CD, suggesting that differences exist among commonly prescribed medication classes. While ACEIs were associated with an overall worse disease course at 5 and 10 years, patients taking ARBs were noted to have fewer instances of corticosteroid use at 10 years. Future large-scale studies are needed to further explore this association.Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved. - Keywords: -raw_completion_output: |- - genes: N/A (no genes mentioned in the text) - exposures: angiotensin-converting enzyme inhibitor (ACEI), angiotensin receptor blocker (ARB) - gene_exposures_relationships: N/A (no gene-molecular activity relationships mentioned in the text) -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - N/A (no gene-molecular activity relationships mentioned in the text) - - === - -extracted_object: - genes: - - N/A (no genes mentioned in the text) - exposures: - - angiotensin-converting enzyme inhibitor (ACEI), angiotensin receptor blocker - (ARB) - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: The role of complex interactions between the intestinal flora and host in regulating intestinal homeostasis and inflammatory bowel disease. - Abstract: Pharmacological treatment of inflammatory bowel disease (IBD) is inefficient and difficult to discontinue appropriately, and enterobacterial interactions are expected to provide a new target for the treatment of IBD. We collected recent studies on the enterobacterial interactions among the host, enterobacteria, and their metabolite products and discuss potential therapeutic options. Intestinal flora interactions in IBD are affected in the reduced bacterial diversity, impact the immune system and are influenced by multiple factors such as host genetics and diet. Enterobacterial metabolites such as SCFAs, bile acids, and tryptophan also play important roles in enterobacterial interactions, especially in the progression of IBD. Therapeutically, a wide range of sources of probiotics and prebiotics exhibit potential therapeutic benefit in IBD through enterobacterial interactions, and some have gained wide recognition as adjuvant drugs. Different dietary patterns and foods, especially functional foods, are novel therapeutic modalities that distinguish pro-and prebiotics from traditional medications. Combined studies with food science may significantly improve the therapeutic experience of patients with IBD. In this review, we provide a brief overview of the role of enterobacteria and their metabolites in enterobacterial interactions, discuss the advantages and disadvantages of the potential therapeutic options derived from such metabolites, and postulate directions for further research.Copyright © 2023 Li, Xu, Cheng, Chen, Yi, Xiao, Zhao, Chen, Tian, Meng, Tang, Zhou, Ruan and Wei. - Keywords: IBD therapies; functional foods; gut metabolome; inflammatory bowel disease; intestinal flora; intestinal homeostasis; short chain fatty acids (SCFAs) -raw_completion_output: |- - genes: N/A - exposures: intestinal flora, enterobacteria, metabolite products, SCFAs, bile acids, tryptophan, probiotics, prebiotics, dietary patterns, functional foods, gut metabolome - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - intestinal flora, enterobacteria, metabolite products, SCFAs, bile acids, tryptophan, - probiotics, prebiotics, dietary patterns, functional foods, gut metabolome - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: Study of the roles of caspase-3 and nuclear factor kappa B in myenteric neurons in a P2X7 receptor knockout mouse model of ulcerative colitis. - Abstract: The literature indicates that the enteric nervous system is affected in inflammatory bowel diseases (IBDs) and that the P2X7 receptor triggers neuronal death. However, the mechanism by which enteric neurons are lost in IBDs is unknown.To study the role of the caspase-3 and nuclear factor kappa B (NF-κB) pathways in myenteric neurons in a P2X7 receptor knockout (KO) mouse model of IBDs.Forty male wild-type (WT) C57BL/6 and P2X7 receptor KO mice were euthanized 24 h or 4 d after colitis induction by 2,4,6-trinitrobenzene sulfonic acid (colitis group). Mice in the sham groups were injected with vehicle. The mice were divided into eight groups (n = 5): The WT sham 24 h and 4 d groups, the WT colitis 24 h and 4 d groups, the KO sham 24 h and 4 d groups, and the KO colitis 24 h and 4 d groups. The disease activity index (DAI) was analyzed, the distal colon was collected for immunohistochemistry analyses, and immunofluorescence was performed to identify neurons immunoreactive (ir) for calretinin, P2X7 receptor, cleaved caspase-3, total caspase-3, phospho-NF-κB, and total NF-κB. We analyzed the number of calretinin-ir and P2X7 receptor-ir neurons per ganglion, the neuronal profile area (µm²), and corrected total cell fluorescence (CTCF).Cells double labeled for calretinin and P2X7 receptor, cleaved caspase-3, total caspase-3, phospho-NF-κB, or total NF-κB were observed in the WT colitis 24 h and 4 d groups. The number of calretinin-ir neurons per ganglion was decreased in the WT colitis 24 h and 4 d groups compared to the WT sham 24 h and 4 d groups, respectively (2.10 ± 0.13 vs 3.33 ± 0.17, P < 0.001; 2.92 ± 0.12 vs 3.70 ± 0.11, P < 0.05), but was not significantly different between the KO groups. The calretinin-ir neuronal profile area was increased in the WT colitis 24 h group compared to the WT sham 24 h group (312.60 ± 7.85 vs 278.41 ± 6.65, P < 0.05), and the nuclear profile area was decreased in the WT colitis 4 d group compared to the WT sham 4 d group (104.63 ± 2.49 vs 117.41 ± 1.14, P < 0.01). The number of P2X7 receptor-ir neurons per ganglion was decreased in the WT colitis 24 h and 4 d groups compared to the WT sham 24 h and 4 d groups, respectively (19.49 ± 0.35 vs 22.21 ± 0.18, P < 0.001; 20.35 ± 0.14 vs 22.75 ± 0.51, P < 0.001), and no P2X7 receptor-ir neurons were observed in the KO groups. Myenteric neurons showed ultrastructural changes in the WT colitis 24 h and 4 d groups and in the KO colitis 24 h group. The cleaved caspase-3 CTCF was increased in the WT colitis 24 h and 4 d groups compared to the WT sham 24 h and 4 d groups, respectively (485949 ± 14140 vs 371371 ± 16426, P < 0.001; 480381 ± 11336 vs 378365 ± 4053, P < 0.001), but was not significantly different between the KO groups. The total caspase-3 CTCF, phospho-NF-κB CTCF, and total NF-κB CTCF were not significantly d -raw_completion_output: |- - genes: caspase-3, nuclear factor kappa B (NF-κB), P2X7 receptor - exposures: 2,4,6-trinitrobenzene sulfonic acid - gene_exposures_relationships: P2X7 receptor triggers neuronal death -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - P2X7 receptor triggers neuronal death - - === - -extracted_object: - genes: - - caspase-3, nuclear factor kappa B (NF-κB), P2X7 receptor - exposures: - - 2,4,6-trinitrobenzene sulfonic acid - gene_exposures_relationships: - - molecular_activity: triggers neuronal death - gene: P2X7 receptor -input_text: |- - Title: Crohn's disease in human immunodeficiency virus-infected patient: A case report. - Abstract: Inflammatory bowel disease (IBD) is an autoimmune condition treated with immunosuppressive drugs. However, the need for immune system suppression becomes questionable when infection with the human immunodeficiency virus (HIV) occurs simultaneously and impacts the course of IBD. Our reported case represents the clinical course, prescribed treatment and its effect, as well as clinical challenges faced by physicians in a combination of such diseases. We also present a comprehensive literature review of similar cases.A 49-year-old woman suffering from a newly diagnosed Crohn's disease was hospitalized due to exacerbated symptoms (abdominal pain, fever, and weight loss). During her hospital stay, she tested positive for HIV. With conservative treatment, the patient improved and was discharged. In the outpatient clinic, her HIV infection was confirmed as stage C3, and antiretroviral treatment was initiated immediately. That notwithstanding, soon the patient was rehospitalized with pulmonary embolism and developed a series of complications because of the subsequent coexistence of IBD and HIV. After intensive and meticulous treatment, the patient's condition has improved and she remains in remission.The paucity of studies and data on the coexistence of HIV and IBD leaves clinicians doubting the optimal treatment options.©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved. - Keywords: Case report; Crohn’s disease; Human immunodeficiency virus; Immunocompromised patient; Inflammatory bowel disease -raw_completion_output: |- - genes: None mentioned in the text - exposures: immunosuppressive drugs, human immunodeficiency virus (HIV), antiretroviral treatment - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - immunosuppressive drugs, human immunodeficiency virus (HIV), antiretroviral - treatment - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: A peculiar case of intususception in a pregnant woman: A diagnostic challenge. - Abstract: Adult intussusception presents a diagnostic challenge given its non-specific symptoms. It is not as common as in infants and young children. Traditionally, diagnostic steps are invariably fit for normal adults, but not in pregnancy which faces certain limitations. A 40-year-old pregnant mother, gravida 9 para 8 at 34-week gestation, complained of intermittent epigastric pain for 2 days, requiring hospitalization. She soon developed minimal per rectal bleeding that was ruled out as hemorrhoid. Imaging was limited due to her pregnancy status. She later developed spontaneous delivery to a premature baby. Computed tomography (CT) revealed an ileocolic intussusception, which was confirmed via exploratory laparotomy. Histology was consistent with inflammatory fibroid polyp. Acute abdomen in pregnancy can be due to various causes, thus a high index of suspicion and early CT abdomen might help in early diagnosis and treatment. The benefit of doing CT on the mother and the risk of CT on the fetus is to be weighed as the timely diagnosis can prevent bowel ischemia and reduce maternal morbidity and mortality. Surgery remains the definite management in adult intussusception and an exact diagnosis can be made during the operation.© 2023 The Authors. Published by Elsevier Inc. on behalf of University of Washington. - Keywords: Abdominal neoplasms; Cecal diseases; Ileal diseases; Intussusception; Pregnant; case report -raw_completion_output: |- - genes: None mentioned in the text - exposures: None mentioned in the text - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - None mentioned in the text - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: DietaAnti-Inflamatoria or DAIN: A Crohn's disease management strategy tailored for Puerto Ricans. - Abstract: Diet has been increasingly shown to be of therapeutic benefit for patients with inflammatory bowel diseases (IBD), especially Crohn's disease (CD). Yet dietary guidelines are nonexistent. Moreover, diets tailored to Puerto Ricans with IBD living on the island, have not been developed and tested. The rising prevalence of IBD in Puerto Rico warrants exploring the use of diet as part of the treatment strategies for these patients [1]. Here, we describe the study design of "Dieta Anti-Inflamatoria" or DAIN, a parallel two-arm randomized pilot trial aiming at testing the efficacy of IBD-Anti-inflammatory diet (IBD-AID) adapted for adults with CD living in Puerto Rico (clinical trial registration number: NCT05627128). We tailored the IBD-AID to the local cuisine preferences and food availability by creating and adapting recipes consistent with the IBD-AID principles [2,3]. In focus groups with a Community Research Advisory Panel and one-on-one consultations with implementation experts, we identified several aspects of the intervention to adapt before the implementation. The objectives of the stakeholder/expert-informed adaptation were to improve feasibility and compliance while developing the culturally tailored dietary intervention. DAIN was designed for adults living in Puerto Rico with CD and geared to be affordable, appropriate, and acceptable for patients with mild-to-moderate CD. The significance of this work is the validation of culturally appropriate nutritional guidelines to help manage CD symptoms. DAIN provides a blueprint for a comprehensive nutritional program that can be adapted to regional preferences and local food availability allowing wider implementation of diet as an adjunct treatment in diverse clinical settings.© 2023 The Authors. Published by Elsevier Inc. - Keywords: -raw_completion_output: |- - genes: None mentioned in the text - exposures: diet, IBD-Anti-inflammatory diet (IBD-AID), local cuisine, food availability, culturally tailored dietary intervention - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - diet, IBD-Anti-inflammatory diet (IBD-AID), local cuisine, food availability, - culturally tailored dietary intervention - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Time to incorporate pre-emptive NUDT15 testing before starting thiopurines in inflammatory bowel disease in Asia and beyond: a review. - Abstract: Thiopurine toxicity is related to genetic polymorphism. Thiopurine methyltransferase (TPMT) variants do not explain thiopurine toxicity in more than half of patients. Asian people, despite the low prevalence of TPMT variants, are more susceptible to thiopurine toxicity. Since 2014, studies from many Asian countries have shown a strong association between nucleoside diphosphate-linked moiety X-type motif (NUDT) 15 polymorphism and thiopurine-induced myelotoxicity.An English language literature search was performed for TPMT and NUDT15 genetic variants in inflammatory bowel disease and other diseases. This article discusses the merits of preemptive NUDT15 and TPMT testing in Asian and non-Asian IBD populations.The NUDT polymorphism occurs in up to 27% of the Asian and Hispanic population. The hematological toxicity occurs in up to a third of patients with this genetic variant. Given this, preemptive testing for NUDT15 variant is worthwhile and is probably more cost-effective than TPMT testing in these groups. Prevalence of NUDT15 variants is low in non-Finnish European population but NUDT15 variants have been linked to myelotoxicity along with TPMT genetic variants. NUDT15 preemptive testing should be considered in the migrant Asian population in Europe and North America and in Caucasian populations who develop myelotoxicity. - Keywords: Crohn’s disease; Inflammatory bowel disease; Thiopurine toxicity in asian; Ulcerative colitis; thiopurine metabolism; thiopurine toxicity; thiopurines -raw_completion_output: |- - genes: TPMT, NUDT15 - exposures: nucleoside diphosphate-linked moiety X-type motif (NUDT) 15 polymorphism, thiopurines - gene_exposures_relationships: TPMT variants and thiopurine toxicity, NUDT15 polymorphism and thiopurine-induced myelotoxicity -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - TPMT variants and thiopurine toxicity, NUDT15 polymorphism and thiopurine-induced myelotoxicity - - === - -extracted_object: - genes: - - TPMT, NUDT15 - exposures: - - nucleoside diphosphate-linked moiety X-type motif (NUDT) 15 polymorphism, thiopurines - gene_exposures_relationships: - - molecular_activity: thiopurine-induced myelotoxicity - gene: HGNC:23063 -named_entities: - - id: HGNC:23063 - label: NUDT15 -input_text: |- - Title: Langerhans Cell Histiocytosis Caused by Adalimumab for Crohn's Disease: A Case Report. - Abstract: - Keywords: -raw_completion_output: |- - genes: not mentioned in the text - exposures: Adalimumab - gene_exposures_relationships: not mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - not mentioned in the text - - === - -extracted_object: - genes: - - not mentioned in the text - exposures: - - Adalimumab - gene_exposures_relationships: - - molecular_activity: not mentioned in the text - gene: not mentioned in the text -input_text: |- - Title: Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities. - Abstract: Interactions among microbes within microbial communities have been shown to play crucial roles in human health. In spite of recent progress, low-level knowledge of bacteria driving microbial interactions within microbiomes remains unknown, limiting our ability to fully decipher and control microbial communities.We present a novel approach for identifying species driving interactions within microbiomes. Bakdrive infers ecological networks of given metagenomic sequencing samples and identifies minimum sets of driver species (MDS) using control theory. Bakdrive has three key innovations in this space: (i) it leverages inherent information from metagenomic sequencing samples to identify driver species, (ii) it explicitly takes host-specific variation into consideration, and (iii) it does not require a known ecological network. In extensive simulated data, we demonstrate identifying driver species identified from healthy donor samples and introducing them to the disease samples, we can restore the gut microbiome in recurrent Clostridioides difficile (rCDI) infection patients to a healthy state. We also applied Bakdrive to two real datasets, rCDI and Crohn's disease patients, uncovering driver species consistent with previous work. Bakdrive represents a novel approach for capturing microbial interactions.Bakdrive is open-source and available at: https://gitlab.com/treangenlab/bakdrive.© The Author(s) 2023. Published by Oxford University Press. - Keywords: -raw_completion_output: |- - genes: Not mentioned in the text. - - exposures: Not mentioned in the text. - - gene_exposures_relationships: Not mentioned in the text. -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Not mentioned in the text. - - === - -extracted_object: - genes: - - Not mentioned in the text. - exposures: - - Not mentioned in the text. - gene_exposures_relationships: - - molecular_activity: Not mentioned in the text. - gene: Not mentioned in the text. -input_text: |- - Title: Efficacy of Crohn's disease exclusion diet in treatment -naïve children and children progressed on biological therapy: a retrospective chart review. - Abstract: Recent trials suggested that the Crohn's disease (CD) exclusion diet (CDED) plus partial enteral nutrition (PEN) is a safe and effective strategy in remission induction of paediatric-onset CD. However, real-world evidence regarding the safety and efficacy of the CDED plus PEN approach is still lacking. The present case-series study reported our experience with the outcomes of CDED plus PEN in the paediatric-onset CD at disease onset and after the loss of response to biologics.We conducted a retrospective chart review on children who were treated with CDED plus PEN through the period from July 2019 and December 2020. Clinical and laboratory data were retrieved and compared at baseline, 6, 12, and 24 weeks of treatment. The primary endpoint of the present study was the rate of clinical remission.The present study retrieved the data from 15 patients. Of them, nine patients were treatment naïve at the time of initiation of CDED plus PEN (group A) and the remaining patients relapsed on biologics before treatment. All patients in groups A and B exhibited clinical remission in week six, which was sustained until week 12. At the end of the follow-up, the clinical remission rate was 87% and 60% in groups A and B, respectively. No side effects were observed in both groups. In group A, the faecal calprotectin (FC) and albumin improved at week six, week 12, and week 24 (p < 0.05). The erythrocyte sedimentation rate (ESR) improved significantly at week 12 (p = 0.021) and week 24 (p = 0.027). At the same time, the haemoglobin and iron levels showed significant improvement only at week 24. For group B, only FC showed numerical reductions over time that did not reach the level of statistical significance.Treatment with CDED plus PEN was well tolerated and achieved an excellent clinical remission rate in treatment-naive patients. However, the benefit of CDED plus PEN was less in patients who initiated the strategy after losing the response to biologics.© 2023. The Author(s). - Keywords: Crohn’s disease; Crohn’s disease exclusion diet; Paediatrics; Partial enteral nutrition; Remission -raw_completion_output: |- - genes: CD - exposures: Crohn's disease exclusion diet (CDED), partial enteral nutrition (PEN), biologics - gene_exposures_relationships: CD-CDED, CD-PEN, CD-biologics -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - CD-CDED, CD-PEN, CD-biologics - - === - -extracted_object: - genes: - - HGNC:2505 - exposures: - - Crohn's disease exclusion diet (CDED), partial enteral nutrition (PEN), biologics - gene_exposures_relationships: - - molecular_activity: CD-biologics - gene: biologics -named_entities: - - id: HGNC:2505 - label: CD -input_text: |- - Title: Spondyloarthritis with inflammatory bowel disease: the latest on biologic and targeted therapies. - Abstract: Spondyloarthritis (SpA) encompasses a heterogeneous group of chronic inflammatory diseases that can affect both axial and peripheral joints, tendons and entheses. Among the extra-articular manifestations, inflammatory bowel disease (IBD) is associated with considerable morbidity and effects on quality of life. In everyday clinical practice, treatment of these conditions requires a close collaboration between gastroenterologists and rheumatologists to enable early detection of joint and intestinal manifestations during follow-up and to choose the most effective therapeutic regimen, implementing precision medicine for each patient's subtype of SpA and IBD. The biggest issue in this field is the dearth of drugs that are approved for both diseases, as only TNF inhibitors are currently approved for the treatment of full-spectrum SpA-IBD. Janus tyrosine kinase inhibitors are among the most promising drugs for the treatment of peripheral and axial SpA, as well as for intestinal manifestations. Other therapies such as inhibitors of IL-23 and IL-17, phosphodiesterase 4 inhibitor, α4β7 integrin blockers and faecal microbiota transplantation seem to only be able to control some disease domains, or require further studies. Given the growing interest in the development of novel drugs to treat both conditions, it is important to understand the current state of the art and the unmet needs in the management of SpA-IBD.© 2023. Springer Nature Limited. - Keywords: -raw_completion_output: |- - genes: TNF, Janus tyrosine kinase, IL-23, IL-17, phosphodiesterase 4, α4β7 integrin - exposures: TNF inhibitors, Janus tyrosine kinase inhibitors, inhibitors of IL-23 and IL-17, phosphodiesterase 4 inhibitor, α4β7 integrin blockers, faecal microbiota transplantation - gene_exposures_relationships: TNF inhibitors - SpA-IBD treatment; Janus tyrosine kinase inhibitors - peripheral and axial SpA treatment and treatment of intestinal manifestations; inhibitors of IL-23 and IL-17 - control of some disease domains, potential treatment but require further studies; phosphodiesterase 4 inhibitor - potential treatment but require further studies; α4β7 integrin blockers - potential treatment but require further studies; faecal microbiota transplantation - potential treatment but require further studies -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - faecal microbiota transplantation - potential treatment but require further studies - - === - -extracted_object: - genes: - - TNF, Janus tyrosine kinase, IL-23, IL-17, phosphodiesterase 4, α4β7 integrin - exposures: - - TNF inhibitors, Janus tyrosine kinase inhibitors, inhibitors of IL-23 and IL-17, - phosphodiesterase 4 inhibitor, α4β7 integrin blockers, faecal microbiota transplantation - gene_exposures_relationships: - - molecular_activity: TNF inhibitors - gene: SpA-IBD treatment - - molecular_activity: Janus tyrosine kinase inhibitors - gene: not mentioned in the text - - molecular_activity: inhibitors of IL-23 and IL-17 - gene: HGNC:5981 - - molecular_activity: phosphodiesterase 4 inhibitor - gene: None - - molecular_activity: α4β7 integrin blockers - gene: N/A -named_entities: - - id: HGNC:5981 - label: IL-17 -input_text: |- - Title: [Mechanism of intestinal injury induced by WNT2B high-expressed fibroblasts in Crohn's disease]. - Abstract: Objective: To explore the mechanism of intestinal tissue damage induced by macrophages activated by WNT2B high-expressed fibroblasts. Methods: This study involved biological information analysis, pathological tissue research and cell experimental research. The biological information of the colon tissue from the children with inflammatory bowel disease in previous study was analyzed again with single-cell sequencing. The pathological tissues were collected by colonoscopy from 10 children with Crohn's disease treated in the Department of Gastroenterology of Guangzhou Women and Children's Medical Center from July 2022 to September 2022. According to the findings of colonoscopy, tissues with obvious inflammation or ulceration were classified as the inflammatory group, while tissues with slight inflammation and no ulceration were classified as the non-inflammatory group. HE staining was performed to observe the pathological changes of the colon tissues. Macrophage infiltration and CXCL12 expression were detected by immunofluorescence. In terms of cell experiments, fibroblasts transfected with WNT2B plasmid or empty plasmid were co-cultured with salinomycin treated or non-treated macrophages, respectively; the expression of proteins through Wnt classical pathway were detected by western blotting. Macrophages treated with SKL2001 were used as the experimental group, and those with phosphate buffer as the control group. The expression and secretion of CXCL12 in macrophages were detected by quantitative Real-time PCR and enzyme-linked immunosorbent assay (ELISA). T-test or rank sum test were used for the comparison between groups. Results: Single-cell sequencing analysis suggested that macrophages were the main cells in inflammatory bowel disease colon tissue, and there was interaction between WNT2B high-expressed fibroblasts and macrophages. HE staining of the 10 patients ((9.3±3.8) years old, 7 males and 3 females) showed that the pathological score of colon tissue in the inflammatory group was higher than that in the non-inflammatory group (4 (3, 4) vs. 2 (1, 2) points, Z=3.05, P=0.002). Tissue immunofluorescence indicated that the number of infiltrating macrophages in the inflammatory group was significantly higher than that in the non-inflammatory group under high power field of view (72.8±10.4 vs.8.4±3.5, t=25.10, P<0.001), as well as the number of cells expressing CXCL12 (14.0±3.5 vs. 4.7±1.9, t=14.68, P<0.001). In cell experiments, western blotting suggested an elevated level of glycogen synthase kinase-3β phosphorylation in macrophages co-cultured with fibroblast transfected with WNT2B plasmid, and salinmycin could reverse this change. Real-time PCR suggested that the transcription level of CXCL12 in the experimental group was higher than that in the control group (6.42±0.04 vs. 1.00±0.03, t=183.00, P<0.001), as well as the expression -raw_completion_output: |- - genes: WNT2B, CXCL12, glycogen synthase kinase-3β - exposures: salinomycin, SKL2001, phosphate buffer - gene_exposures_relationships: WNT2B to macrophage activation, fibroblast transfected with WNT2B plasmid to elevated level of glycogen synthase kinase-3β phosphorylation, salinomycin to reversal of glycogen synthase kinase-3β phosphorylation change, SKL2001 to macrophage treatment, phosphate buffer as control group. -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - WNT2B to macrophage activation, fibroblast transfected with WNT2B plasmid to elevated level of glycogen synthase kinase-3β phosphorylation, salinomycin to reversal of glycogen synthase kinase-3β phosphorylation change, SKL2001 to macrophage treatment, phosphate buffer as control group. - - === - -extracted_object: - genes: - - WNT2B, CXCL12, glycogen synthase kinase-3β - exposures: - - salinomycin, SKL2001, phosphate buffer - gene_exposures_relationships: - - molecular_activity: macrophage treatment - gene: SKL2001 -input_text: |- - Title: Sialylation shapes mucus architecture inhibiting bacterial invasion in the colon. - Abstract: In the intestine, Mucin 2 (Muc2) forms a network structure and prevents bacterial invasion. Glycans are indispensable for Muc2 barrier function. Among various glycosylation patterns of Muc2, sialylation inhibits a bacteria-dependent Muc2 degradation. However, the mechanisms by which Muc2 creates the network structure and sialylation prevents the mucin degradation remain unknown. Here, by focusing on two colon-specific glycosyltransferases, St6galnac6 and B3galt5, mediating the generation of disialylated glycans, we show that sialylation forms the network structure of Muc2 by providing negative charge and hydrophilicity. The colonic mucus of mice lacking St6galnac6 and B3galt5 was less sialylated, thinner, and more permeable to microbiota, resulting in high susceptibility to intestinal inflammation. Mice with a B3galt5 mutation associated with inflammatory bowel disease (IBD) also showed the loss of disialylated glycans of mucus and the high susceptibility to intestinal inflammation, suggesting that the reduced sialylation of Muc2 is associated with the pathogenesis of IBD. In mucins of mice with reduced sialylation, negative charge was reduced, the network structure was disturbed, and many bacteria invaded. Thus, sialylation mediates the negative charging of Muc2 and facilitates crosslinking of Muc2 polymers to form the network structure, and thereby inhibits bacterial invasion in the colon to maintain gut homeostasis.Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved. - Keywords: -raw_completion_output: |- - genes: Mucin 2 (Muc2), St6galnac6, B3galt5 - - exposures: sialylation - - gene_exposures_relationships: Muc2 to sialylation -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Muc2 to sialylation - - === - -extracted_object: - genes: - - HGNC:7512 - exposures: - - sialylation - gene_exposures_relationships: - - molecular_activity: sialylation - gene: HGNC:7512 -named_entities: - - id: HGNC:7512 - label: Mucin 2 (Muc2), St6galnac6, B3galt5 -input_text: |- - Title: Adiponectin Levels in Inflammatory Bowel Disease - A Systematic Review and Meta-analysis. - Abstract: Adipose tissue plays an important role in the pathogenesis of inflammatory conditions. The role of adipokines in inflammatory bowel disease (IBD) has been evaluated in the current literature with conflicting results. The aim of this study was to evaluate adiponectin levels in IBD patients, including Crohn's disease (CD) and ulcerative colitis (UC), compared to controls, as well as further subgroup analyses. Hence, assessing the potential role of adiponectin as a surrogate marker.We performed a systematic electronic search on PubMed, EMBASE, Scopus and Cochrane Library, including observational or interventional studies evaluating serum or plasma adiponectin levels in IBD patients on humans. The primary summary outcome was the mean difference (MD) in serum or plasma adiponectin levels between IBD patients vs. controls. Subgroups analyses were conducted involving adiponectin levels in CD and UC compared to controls, as well as CD compared to UC.A total of 20 studies were included in our qualitative synthesis and 14 studies in our quantitative synthesis, with a total population sample of 2,085 subjects. No significant MD in serum adiponectin levels was observed between IBD patients vs. controls (-1.331 [95% CI -3.135-0.472]), UC patients vs. controls (-0.213 [95% CI -1.898-1.472]), and CD patients vs. controls (-0.851 [95% CI -2.263-0.561]). Nevertheless, a significant MD was found between UC patients vs. CD patients (0.859 [95% CI 0.097-1.622]).Serum adiponectin levels were not able to differentiate between IBD, UC and CD patients compared to controls. However, significantly higher serum adiponectin levels were observed in UC compared to CD patients.S. Karger AG, Basel. - Keywords: -raw_completion_output: |- - genes: None mentioned in the text - exposures: adiponectin - gene_exposures_relationships: None mentioned in the text -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - adiponectin - gene_exposures_relationships: - - molecular_activity: None mentioned in the text - gene: None mentioned in the text -input_text: |- - Title: Clinical course of new-onset Crohn's disease in children and adolescents in dependency of age, initial location, initial severity level and therapy over the period 2000-2014 based on the Saxon Pediatric IBD-Registry in Germany. - Abstract: In Saxony, the incidence of Crohn's disease (CD) in children and adolescents increased significantly from 3.3 per 100,000 person-years in 2000 to 5.1 in 2014. The aim of this study was to describe the initial characteristics and the clinical course of CD in children and adolescents and to identify drug treatment options associated with an advantage for a mild course or remission.Clinical data were collected from patients who suffered from inflammatory bowel disease (IBD) and were recruited in the Saxon Pediatric IBD-Registry. All children newly diagnosed with CD in this registry in Saxony between 2000 and 2014 were included in this registry study. Characteristics such as age, disease location and extra-intestinal manifestations at diagnosis were accessed. The severity level of the disease at diagnosis as well as at follow-up were analysed by PCDAI index. Patients were divided into 3 groups according to length of follow-up: 1-3 years, 4-6 years and 7-9 years after diagnosis. A logistic regression model was conducted to examine which baseline parameters are associated with disease progression.There were 338 children and adolescents with CD included in this registry study. At diagnosis, the median age of patients was 12.0 (0.7-14.9), 61.5% (n = 208) of the patients were male. The most common disease location observed in pediatric CD patients was the L3 (55%, n = 176). Patients aged 10-14 years were significantly more likely to present an L2 than patients aged 0-4 years (80.3%, n = 53 vs. 19.7%, n = 13, p = 0.01). During the follow-up, data from 71.3% (n = 241) othe patients were available. Disease activity measured by PCDAI decreased in 47.7% (n = 115) of the patients, 40.7% (n = 98) of the patients were stable and increased in 11.6% (n = 28) of the patients. Patients with intermediate/severe disease at onset were more likely to have an active disease at the end of follow up, too (p = 0.00). Logistic regression analysis of the initial characteristics showed that the age at diagnosis, gender, initial location and initial extra-intestinal manifestation are not associated with the progression of the disease (p>0.05). Furthermore, drug treatment options could be identified from our data, which are associated with benefits for a milder course or remission.From 2000 to 2014, the health status of most pediatric patients with CD had improved or remained stable. Initial characteristics including age at diagnosis, initial localization and initial extra-intestinal manifestation are not associated with the progression of the disease, only the initial activity by PCDAI.Copyright: © 2023 Dong et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestr -raw_completion_output: |- - genes: None mentioned in the text - exposures: drug treatment options - gene_exposures_relationships: None relevant -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None relevant - - === - -extracted_object: - genes: - - None mentioned in the text - exposures: - - drug treatment options - gene_exposures_relationships: - - molecular_activity: None relevant - gene: None relevant -input_text: |- - Title: Nutritional aspects of inflammatory bowel disease. - Abstract: The number of people diagnosed with inflammatory bowel disease (IBD) continues to increase in most parts of the world. Although the exact etiology of this chronic intestinal disease is not fully understood, nutritional factors appear to play key roles. Furthermore, individuals with IBD are at increased risk of adverse nutritional impacts, including micronutrient deficiencies.This review aims to summarize recent reports focusing on nutritional factors relevant to the development of IBD and to also review data on nutritional deficiencies seen in individuals with IBD.The typical Western diet, characterized by high-fat/high-sugar foods, along with food additives, appears to contribute to the etiopathogenesis of IBD. In contrast, some reports indicate that some foods are likely protective. However, there are inconsistencies in the currently available data, reflecting study design and other confounding factors. Furthermore, some of the conclusions are inferred from animal or in vitro studies. The presence of IBD can compromise the nutrition of individuals with one of these disorders: ongoing monitoring is critical. Nutrition and diet in the setting of IBD remain key areas for further and ongoing study. - Keywords: Crohn disease; Diet; Inflammation; Inflammatory bowel disease; Nutrition; ulcerative colitis -raw_completion_output: |- - genes: Crohn disease; ulcerative colitis - exposures: nutritional factors; high-fat/high-sugar foods; food additives - gene_exposures_relationships: Crohn disease - nutrition; ulcerative colitis - nutrition -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - ulcerative colitis - nutrition - - === - -extracted_object: - genes: - - Crohn disease - - ulcerative colitis - exposures: - - nutritional factors - - high-fat/high-sugar foods - - CHEBI:64047 - gene_exposures_relationships: - - molecular_activity: nutrition - gene: Crohn disease - - molecular_activity: nutrition - gene: ulcerative colitis -named_entities: - - id: CHEBI:64047 - label: food additives -input_text: |- - Title: Incisional hernia rates between intracorporeal and extracorporeal anastomosis in minimally invasive ileocolic resection for Crohn's disease. - Abstract: One-third of patients with Crohn's disease (CD) require multiple surgeries during their lifetime. So, reducing the incisional hernia rate is crucial. We aimed to define incisional hernia rates after minimally invasive ileocolic resection for CD, comparing intracorporeal anastomosis with Pfannenstiel incision (ICA-P) versus extracorporeal anastomosis with midline vertical incision (ECA-M).This retrospective cohort compares ICA-P versus ECA-M from a prospectively maintained database of consecutive minimally invasive ileocolic resections for CD performed between 2014 and 2021 in a referral center.Of the 249 patients included: 59 were in the ICA-P group, 190 in the ECA-M group. Both groups were similar according to baseline and preoperative characteristics. Overall, 22 (8.8%) patients developed an imaging-proven incisional hernia: seven at the port-site and 15 at the extraction-site. All 15 extraction-site incisional hernias were midline vertical incisions [7.9%; p = 0.025], and 8 patients (53%) required surgical repair. Time-to-event analysis showed a 20% rate of extraction-site incisional hernia in the ECA-M group after 48 months (p = 0.037). The length of stay was lower in the intracorporeal anastomosis with Pfannenstiel incision group [ICA-P: 3.3 ± 2.5 vs. ECA-M: 4.1 ± 2.4 days; p = 0.02] with similar 30-day postoperative complication [11(18.6) vs. 59(31.1); p = 0.064] and readmission rates [7(11.9) vs. 18(9.5); p = 0.59].Patients in the ICA-P group did not encounter any incisional hernias while having shorter hospital length of stay and similar 30-day postoperative complications or readmission compared to ECA-M. Therefore, more consideration should be given to performing intracorporeal anastomosis with Pfannenstiel incision during Ileocolic resection in patients with CD to reduce hernia risk.© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature. - Keywords: Anastomosis; Crohn disease; Ileocolic resection; Incisional hernia; Minimally invasive surgery -raw_completion_output: |- - genes: N/A - exposures: Pfannenstiel incision, midline vertical incision, intracorporeal anastomosis, extracorporeal anastomosis - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - Pfannenstiel incision, midline vertical incision, intracorporeal anastomosis, - extracorporeal anastomosis - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -input_text: |- - Title: The Tolerance of Gut Commensal Faecalibacterium to Oxidative Stress Is Strain Dependent and Relies on Detoxifying Enzymes. - Abstract: Obligate anaerobic bacteria in genus Faecalibacterium are among the most dominant taxa in the colon of healthy individuals and contribute to intestinal homeostasis. A decline in the abundance of this genus is associated with the occurrence of various gastrointestinal disorders, including inflammatory bowel diseases. In the colon, these diseases are accompanied by an imbalance between the generation and elimination of reactive oxygen species (ROS), and oxidative stress is closely linked to disruptions in anaerobiosis. In this work, we explored the impact of oxidative stress on several strains of faecalibacteria. An in silico analysis of complete genomes of faecalibacteria revealed the presence of genes encoding O2- and/or ROS-detoxifying enzymes, including flavodiiron proteins, rubrerythrins, reverse rubrerythrins, superoxide reductases, and alkyl peroxidase. However, the presence and the number of these detoxification systems varied greatly among faecalibacteria. These results were confirmed by O2 stress survival tests, in which we found that strains differed widely in their sensitivity. We showed the protective role of cysteine, which limited the production of extracellular O2•- and improved the survival of Faecalibacterium longum L2-6 under high O2 tension. In the strain F. longum L2-6, we observed that the expression of genes encoding detoxifying enzymes was upregulated in the response to O2 or H2O2 stress but with different patterns of regulation. Based on these results, we propose a first model of the gene regulatory network involved in the response to oxidative stress in F. longum L2-6. IMPORTANCE Commensal bacteria in the genus Faecalibacterium have been proposed for use as next-generation probiotics, but efforts to cultivate and exploit the potential of these strains have been limited by their sensitivity to O2. More broadly, little is known about how commensal and health-associated bacterial species in the human microbiome respond to the oxidative stress that occurs as a result of inflammation in the colon. In this work, we provide insights regarding the genes that encode potential mechanisms of protection against O2 or ROS stress in faecalibacteria, which may facilitate future advances in work with these important bacteria. - Keywords: Faecalibacterium; oxidative stress; oxygen sensitivity; transcriptional regulation -raw_completion_output: |- - genes: flavodiiron proteins; rubrerythrins; reverse rubrerythrins; superoxide reductases; alkyl peroxidase - exposures: oxidative stress; reactive oxygen species (ROS); cysteine; O2 tension; O2; H2O2 stress - gene_exposures_relationships: faecalibacteria have genes encoding O2- and/or ROS-detoxifying enzymes; cysteine limits the production of extracellular O2•- and improves the survival of Faecalibacterium longum L2-6 under high O2 tension; genes encoding detoxifying enzymes are upregulated in response to O2 or H2O2 stress with different patterns of regulation; the genes encode potential mechanisms of protection against O2 or ROS stress in faecalibacteria -prompt: |+ - From the text below, extract the following entities in the following format: - - molecular_activity: - gene: - - - Text: - the genes encode potential mechanisms of protection against O2 or ROS stress in faecalibacteria - - === - -extracted_object: - genes: - - flavodiiron proteins - - rubrerythrins - - reverse rubrerythrins - - superoxide reductases - - alkyl peroxidase - exposures: - - oxidative stress - - CHEBI:26523 - - CHEBI:15356 - - O2 tension - - CHEBI:15379 - - H2O2 stress - gene_exposures_relationships: - - molecular_activity: exposure to high O2 tension. - gene: Faecalibacterium longum L2-6. - - molecular_activity: O2 or H2O2 stress - gene: detoxifying enzymes - - molecular_activity: O2 or ROS stress - gene: faecalibacteria -named_entities: - - id: CHEBI:26523 - label: reactive oxygen species (ROS) - - id: CHEBI:15356 - label: cysteine - - id: CHEBI:15379 - label: O2 -input_text: |- - Title: Review article: Translating STRIDE-II into clinical reality - Opportunities and challenges. - Abstract: With the introduction of novel therapies for inflammatory bowel diseases (IBD), 'treat-to-target' strategies are increasingly discussed to improve the short- and long-term outcomes in IBD patients.To discuss opportunities and challenges of a treat-to-target approach in light of the current 'Selecting Therapeutic Targets in Inflammatory Bowel Disease' (STRIDE-II) consensus.The 2021 update of STRIDE-II encompasses 13 evidence- and consensus-based recommendations for treat-to-target strategies in adults and children with IBD. We highlight the potential implications and limitations of these recommendations for clinical practice.STRIDE-II provides valuable guidance for personalised IBD management. It reflects scientific progress as well as increased evidence of improved outcomes when more ambitious treatment goals such as mucosal healing are achieved.Prospective studies, objective criteria for risk stratification, and better predictors of therapeutic response are needed to potentially render 'treating to target' more effective in the future.© 2023 The Authors. Alimentary Pharmacology & Therapeutics published by John Wiley & Sons Ltd. - Keywords: Crohn’s disease < disease-based; biologics (IBD) < topics; inflammatory bowel disease < disease-based; ulcerative colitis < disease-based -raw_completion_output: |- - genes: - exposures: novel therapies, treatments, therapeutic response - gene_exposures_relationships: None mentioned in the text. -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None mentioned in the text. - - === - -extracted_object: - exposures: - - novel therapies, treatments, therapeutic response - gene_exposures_relationships: - - molecular_activity: None mentioned in the text. - gene: None mentioned in the text. -input_text: |- - Title: Real-world experience with subcutaneous infliximab: broadening treatment strategies for inflammatory bowel disease. - Abstract: The first subcutaneous (SC) formulation of infliximab (IFX), CT‑P13 SC, has been approved in Europe and Australia, including for the treatment of inflammatory bowel disease (IBD).We provide a comprehensive overview of available clinical trial and real-world data for IFX SC treatment of IBD, focusing on potential benefits of switching from IFX intravenous (IV) to IFX SC. We evaluate emerging evidence for IFX SC treatment for difficult-to-treat IBD, use as monotherapy, and suitability for patients receiving escalated IFX IV. Therapeutic drug monitoring approaches and patient and healthcare system perspectives on IFX SC are also discussed.IFX SC represents a significant treatment innovation in the tumor necrosis factor inhibitor class after approximately 20 years of IFX IV availability. Evidence suggests that IFX SC is well tolerated and is associated with high patient acceptance and satisfaction. In addition, effectiveness is maintained in patients with stable disease following switch from IFX IV. Switching may be advisable, given the clinical benefits of IFX SC and its potential to improve healthcare service capacity. There are several areas requiring further research, including the role of IFX SC in difficult-to-treat and refractory disease, and the feasibility of IFX SC monotherapy. - Keywords: Anti-TNF; Crohn’s disease; biologics; inflammatory bowel disease; infliximab; subcutaneous; ulcerative colitis -raw_completion_output: |- - genes: No genes mentioned - exposures: infliximab (IFX), CT‑P13 SC - gene_exposures_relationships: No gene to molecular activity relationships mentioned -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - No gene to molecular activity relationships mentioned - - === - -extracted_object: - genes: - - No genes mentioned - exposures: - - infliximab (IFX), CT‑P13 SC -input_text: |- - Title: Posttranslational modifications of NLRP3 and their regulatory roles in inflammasome activation. - Abstract: The NACHT, LRR, and PYD domains-containing protein 3 (NLRP3) inflammasome is a multimolecular complex that plays a fundamental role in inflammation. Optimal activation of NLRP3 inflammasome is crucial for host defense against pathogens and the maintenance of immune homeostasis. Aberrant NLRP3 inflammasome activity has been implicated in various inflammatory diseases. Posttranslational modifications (PTMs) of NLRP3, a key inflammasome sensor, play critical roles in directing inflammasome activation and controlling the severity of inflammation and inflammatory diseases, such as arthritis, peritonitis, inflammatory bowel disease, atherosclerosis, and Parkinson's disease. Various NLRP3 PTMs, including phosphorylation, ubiquitination, and SUMOylation, could direct inflammasome activation and control inflammation severity by affecting the protein stability, ATPase activity, subcellular localization, and oligomerization of NLRP3 as well as the association between NLRP3 and other inflammasome components. Here, we provide an overview of the PTMs of NLRP3 and their roles in controlling inflammation and summarize potential anti-inflammatory drugs targeting NLRP3 PTMs.© 2023 Wiley-VCH GmbH. - Keywords: NLRP3; inflammasome; inflammation; posttranslational modifications; ubiquitination -raw_completion_output: |- - genes: NLRP3 - exposures: posttranslational modifications - gene_exposures_relationships: NLRP3 to posttranslational modifications -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - NLRP3 to posttranslational modifications - - === - -extracted_object: - genes: - - HGNC:16400 - exposures: - - posttranslational modifications - gene_exposures_relationships: - - molecular_activity: posttranslational modifications - gene: HGNC:16400 -named_entities: - - id: HGNC:16400 - label: NLRP3 -input_text: |- - Title: Chitinase 3-Like-1 Expression Is Upregulated Under Inflammatory Conditions in Human Oral Epithelial Cells. - Abstract: Chitinase 3-like-1 (CHI3L1), also known as YKL-40, is a partially secreted glycoprotein and is involved in inflammatory disorders, including inflammatory bowel diseases. CHI3L1 is known to play a role in biological responses such as cell proliferation, tissue remodeling, and inflammation. CHI3L1 forms an immune complex (known as a Chitosome complex) with IL-13 receptor alpha 2 (IL-13 Rα2) and transmembrane protein 219 (TMEM219) to activate the MAPK/ERK and PKB/AKT signaling pathways. The objective of this study is to investigate how the expressions of CHI3L1 and a Chitosome complex in human oral cavity epithelial cells are linked with intraoral inflammatory diseases.CHI3L1 and Chitosome complex mRNA expressions were analyzed using human oral squamous cancer cell lines, HSC3 and HSC4 cells. Signaling activation in HSC4 cells was analyzed by using the western blot technique. Immunohistological analysis was performed using surgical samples obtained from patients with benign oral cavity tumors and cysts.Increased expression of CHI3L1 was observed in both HSC3 and HSC4 cells after TNFα stimulation. The expression of Chitosome complex factors increased as CHI3L1 levels increased, resulting in the activation of a downstream signaling pathway. Among the intraoral tissues, the epithelial cells from inflammatory lesions, but not benign tumors, were found to be intensively stained with the anti-CHI3L1 antibody.It was indicated that the formation of a Chitosome complex is induced during inflammation, leading to the activation of signaling pathways. - Keywords: chitinase 3-like-1; chitosome complex; inflammation; oral epithelial cells -raw_completion_output: |- - genes: CHI3L1, IL-13 Rα2, TMEM219 - exposures: TNFα, Chitosome complex - gene_exposures_relationships: CHI3L1 - TNFα stimulation; CHI3L1 - Chitosome complex; Chitosome complex - activation of signaling pathways -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - Chitosome complex - activation of signaling pathways - - === - -extracted_object: - genes: - - CHI3L1, IL-13 Rα2, TMEM219 - exposures: - - TNFα, Chitosome complex - gene_exposures_relationships: - - molecular_activity: TNFα stimulation - gene: HGNC:1932 - - molecular_activity: Chitosome complex - gene: HGNC:1932 - - molecular_activity: activation of signaling pathways - gene: Chitosome complex -named_entities: - - id: HGNC:1932 - label: CHI3L1 -input_text: |- - Title: Drug rediscovery in gastroenterology: from off-label to on-label use of thioguanine in inflammatory bowel disease. - Abstract: Drug rediscovery refers to the principle of using 'old' drugs outside the indications mentioned in the summary of product characteristics. In the past decades, several drugs were rediscovered in a wide variety of medical fields. One of the most recent examples is the unconditional registration of thioguanine (TG), a thiopurine derivative, in patients with inflammatory bowel disease in the Netherlands. In this paper, we aim to visualise potential hurdles that hamper drug rediscovery in general, emphasise the global need for optimal use and development of potentially useful drugs, and provide an overview of the registration process for TG in the Netherlands. With this summary, we aim to guide drug rediscovery trajectories in the near future.© Author(s) (or their employer(s)) 2023. No commercial re-use. See rights and permissions. Published by BMJ. - Keywords: azathioprine; crohn's disease; drug development; drug metabolism; inflammatory bowel disease -raw_completion_output: |- - genes: N/A - exposures: thioguanine (TG), thiopurine derivative - gene_exposures_relationships: N/A -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - N/A - - === - -extracted_object: - genes: - - N/A - exposures: - - CHEBI:9516 - gene_exposures_relationships: - - molecular_activity: N/A - gene: N/A -named_entities: - - id: CHEBI:9516 - label: thioguanine (TG), thiopurine derivative -input_text: |- - Title: Author's Reply: ``Use of biologics for the management of Crohn's disease''. - Abstract: - Keywords: -raw_completion_output: |- - genes: None - exposures: None - gene_exposures_relationships: None -prompt: |+ - Split the following piece of text into fields in the following format: - - molecular_activity: - gene: - - - Text: - None - - === - -extracted_object: - genes: - - None - exposures: - - None - gene_exposures_relationships: - - molecular_activity: None - gene: None diff --git a/txt_cases_results.tsv b/txt_cases_results.tsv deleted file mode 100644 index 7523a75b0..000000000 --- a/txt_cases_results.tsv +++ /dev/null @@ -1,1331 +0,0 @@ -input file name correct diagnosis gpt diagnosis -PMID_35704401-case.txt terms “poxvirus,” “outbreak,” and “sexually transmitted infection” revealed a report that had been posted on the same day by public health authorities in the United Kingdom. It described four cases similar to this one, in which a diagnosis of monkeypox had been confirmed. It was at this point that I contacted the infection control unit at our hospital to report my concern that the patient may have monkeypox. "Most likely diagnosis: Lymphogranuloma venereum (Chlamydia trachomatis L1-L3 serovars) - -Differential Diagnoses: -1. Lymphogranuloma venereum -2. Herpes simplex virus infection (HSV-2) -3. Syphilis (Treponema pallidum subspecies pallidum) -4. Gonorrhea (Neisseria gonorrhoeae) -5. Granuloma inguinale (Klebsiella granulomatis) -6. Chancroid (Haemophilus ducreyi) -7. Behcet’s disease -8. Crohn's disease -9. Drug reaction or allergy -10. Steven-Johnson Syndrome " -PMID_34965341-case.txt In summary, this patient’s history suggests that he had a transient ischemic attack, possibly due to moyamoya disease. To establish the diagnosis of moyamoya disease in this case, neuroimaging with angiography should be performed. "Most likely diagnosis: Transient ischemic attack (TIA) - -Differential diagnoses: -1. Transient ischemic attack (TIA) -2. Todd's paralysis -3. Hemiplegic migraine -4. Functional neurological disorder -5. Transient global amnesia -6. Complex partial seizure -7. Metabolic encephalopathy -8. Hyperventilation syndrome -9. Psychogenic non-epileptic seizures -10. Migraine with brainstem aura -11. Sodium channel genetic mutation causing episodic ataxia -12. Panic disorder -13. Early-onset multiple sclerosis -" -PMID_34670047-case.txt available, including radionuclide scanning (with the use of technetium-99m–labeled sestamibi), dynamic CT, magnetic resonance imaging, and ultrasonography. I would opt for ultrasonography in this young patient in order to avoid exposure to the radiation that is inherent with CT and radionuclide scans. How does the finding of hyperparathyroidism influence the diagnosis of the mandibular mass? The possibility of the diagnosis of an atypical ossifying fibroma is increased, given its occurrence in the context of hyperparathyroidism due to CDC73 mutations. Nevertheless, brown tumors are a complication of hyperparathyroidism, and the reported biopsy and radiographic findings are more consistent with this type of lesion. "Most Likely Diagnosis: Primary Hyperparathyroidism due to Parathyroid Adenoma resulting in a central giant cell lesison in mandible. - -Differential Diagnoses (Ranked from most likely to least likely): -1. Primary Hyperparathyroidism due to Parathyroid Adenoma -2. Brown Tumor of Hyperparathyroidism -3. Central Giant Cell Granuloma (CGCG) -4. Cherubism -5. Fibrous Dysplasia -6. Osteosarcoma -7. Metastatic cancer in the mandible -8. Ameloblastoma -9. Primary Parathyroid Carcinoma causing hyperparathyroidism -10. Metabolic bone disease (ex. Paget’s disease of bone) -11. Multifocal Giant Cell Lesion due to Hyperparathyroidism-Jaw Tumor Syndrome (HPT-JT) -12. Neurofibromatosis type 1 (von Recklinghausen disease) with sphenoid dysplasia. -13. Osteomyelitis of the mandible -14. Basal cell nevus syndrome (Gorlin-Goltz syndrome)." -PMID_36416771-case.txt Optic nerve tumor, either optic nerve sheath meningioma or optic nerve glioma. "Most likely diagnosis: -Optic Neuropathy secondary to an immunological reaction, possibly due to a paraneoplastic syndrome - -Differential Diagnosis: -1. Neuromyelitis Optica spectrum disorder (derived from the description of optic neuritis and negative anti-aquaporin-4 antibody test) -2. Acute optic neuritis, atypical variant (because of the response to steroid therapy) -3. Optic neuritis with underlying systemic lupus erythematosus (due to speckled pattern ANA and visual symptoms) -4. Sarcoidosis (the granulomas could cause optic nerve enlargement) -5. Paraneoplastic syndrome such as Collagen vascular disease causing optic neuropathy -6. Infectious cause of optic neuritis such as Lyme disease, Syphilis or Tuberculosis -7. Tumor infiltrating the optic nerve -8. Ischemic optic neuropathy -9. Intracranial hypertension -10. Migraine associated optic neuropathy - -Given the patient's clinical history and current symptoms, some diagnoses are more likely than others. However, the differential diagnosis should be confirmed through further investigations for a definitive diagnosis." -PMID_34644476-case.txt death and a very low chance of recovery without urgent treatment and consideration of bone marrow transplantation. "Most Likely Diagnosis: Severe aplastic anemia - -Differential Diagnoses: -1. Severe aplastic anemia -2. Acute lymphocytic leukemia -3. Myelodysplastic syndrome -4. Acute myeloid leukemia -5. Immune thrombocytopenic purpura -6. Drug-induced thrombocytopenia -7. Thrombotic thrombocytopenic purpura -8. Hemolytic uremic syndrome -9. Disseminated intravascular coagulation -10. Paroxysmal nocturnal hemoglobinuria -11. HIV infection -12. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) related thrombocytopenia. " -PMID_34910867-case.txt medicines and that the diagnostic test was for a blood lead level. "Most likely diagnosis: Acute intermittent porphyria - -Differential diagnoses: - -1. Acute intermittent porphyria -2. Other types of porphyrias like Variegate porphyria or Hereditary coproporphyria -3. Medication-induced acute porphyria attack -4. Paraneoplastic syndrome associated porphyria -5. Psychogenic porphyria -6. Bowel obstruction -7. Chronic malnutrition -8. Isolated hyponatremia -9. Duodenal ulcer from usage of pantoprazole -10. Small Bowel Bacterial Overgrowth syndrome (SIBO) -11. Lead poisoning -12. Iron overload syndrome -13. Celiac disease." -PMID_35020988-case.txt The reported response rate to immunotherapy ranges from 10 to 70%. Combination therapy seems to be more effective than monotherapy. This patient had many of the typical sleep symptoms reported in patients with anti-IgLON5 disease, as well as a combination of neurologic symptoms reported in patients with clinical subtypes of the disease. To establish this diagnosis, testing for IgLON5 autoantibodies was performed. "Most likely diagnosis: - -1. Rapid Eye Movement (REM) sleep behavior disorder and ALS (Amyotrophic lateral sclerosis) - -Differential Diagnoses in order of likelihood: - -1. REM sleep behavior disorder and Motor neuron disease -2. Sleep apnea syndrome with central nervous system disease -3. Progressive Supranuclear Palsy (PSP) -4. Multiple System Atrophy (MSA) -5. Parkinson’s disease (with nighttime behavior and sleep issues) -6. Central Nervous System Lymphoma -7. Creutzfeldt-Jakob disease -8. Vascular dementia -9. Alzheimer’s disease with disturbed sleep patterns -10. Stroke with sleep disorders -11. Paraneoplastic syndrome with sleep disorders -12. Frontotemporal dementia with sleep disturbances -13. Lewy Body Dementia with sleep disturbances." -PMID_36300978-case.txt Sarcoidosis or tuberculosis. "1. Most likely diagnosis: Tuberculous Uveitis - -2. Differential Diagnoses: - - Tuberculous Uveitis - - Sarcoidosis - - Behçet's disease - - Lymphoma - - Secondary Syphilis - - Viral infection (such as CMV or Herpes simplex) - - Toxoplasmosis - - Leukemia" -PMID_33882209-case.txt Varicella–zoster virus infection. "Most likely diagnoses: -Herpes Zoster (Shingles) - -Differential Diagnosis: -1. Herpes Zoster Ophthalmicus -2. Cellulitis -3. Fungal Infection (e.g., Blastomycosis) -4. Cutaneous Lupus Erythematosus -5. Erysipelas -6. Non-melanoma Skin Cancer (e.g., Squamous cell carcinoma, Basal cell carcinoma) -7. Granulomatosis with Polyangiitis (Wegener’s Granulomatosis) -8. Sweet Syndrome -9. Staphylococcal Scalded Skin Syndrome -10. Stevens-Johnson Syndrome -11. Leukemia cutis -12. Lymphoma -13. Cutaneous metastases from an unknown primary cancer -14. Bullous Pemphigoid -15. Dermatitis herpetiformis -16. Aging-associated Dermatosis." -PMID_34010534-case.txt Lactic acidosis. "Most Likely Diagnosis: Diarrhea-associated hemolytic uremic syndrome (HUS) secondary to acute kidney injury and dehydration. - -Differential Diagnosis: -1. Diarrhea-associated hemolytic uremic syndrome (HUS) -2. Acute interstitial nephritis, possibly related to the use of antibiotics -3. Dehydration associated Prerenal acute kidney injury -4. Chronic kidney disease from longstanding hypertension and diabetes mellitus -5. Tubulointerstitial nephritis and uveitis syndrome -6. Septicaemia-induced acute renal failure -7. Urinary tract infection leading to pyelonephritis and resultant kidney injury -8. Ischemic acute tubular necrosis from hypotension (due to heart failure) -9. Diabetic nephropathy, often associated with Type 2 diabetes -10. Rhabdomyolysis-induced acute renal failure, possibly due to the humeral fracture -11. Polycystic kidney disease -12. Contrast-induced nephropathy -13. Cholesterol embolism, often associated with atherosclerotic disease -14. Hypertension-induced end organ damage resulting in kidney failure -15. Gout nephropathy due to use of allopurinol." -PMID_33826823-case.txt Normal pressure hydrocephalus. "Most Likely Diagnosis: Parkinson’s disease - -Differential Diagnosis: -1. Parkinson's Disease -2. Normal pressure hydrocephalus -3. Small Vessel Ischemic Disease -4. Chronic Traumatic Encephalopathy resulting from the previous head trauma -5. Dementia with Lewy bodies -6. Multisystem atrophy -7. Progressive Supranuclear Palsy -8. B12 or folate deficiency related neurologic symptoms -9. Neurosyphilis -10. Early onset Alzheimer's disease -11. Effect of polypharmacy and/or drug side effects -12. Frontotemporal dementia -13. Vascular dementia -14. Geriatric depression with cognitive impairment -15. Creutzfeldt-Jakob disease." -PMID_36546630-case.txt Hepatic adenoma. "Most Likely Diagnosis: Puerperal (Postpartum) Group B Streptococcal Sepsis with a liver abscess - -Differential Diagnoses (ranked by likelihood): - -1. Puerperal (Postpartum) Group B Streptococcal Sepsis with a liver abscess -2. Pyelonephritis secondary to Group B Streptococcus -3. Postpartum Endometritis caused by Group B Streptococcus -4. Hepatic Hematoma (secondary to the post-partum hemorrhage, exacerbated by postnatal NSAIDs usage) -5. Hepatitis (secondary to drug use, like acetaminophen toxicity) -6. Renal calculus with secondary infection -7. Cholecystitis -8. Pancreatitis secondary to gallstones (postpartum gallbladder sludging) -9. Pleural effusion or pneumonia -10. Postpartum Cardiomyopathy leading to hepatic congestion -11. Deep Vein Thrombosis causing Pulmonary Embolism presenting as pleuritic pain." -PMID_36351271-case.txt I suspect that this patient had neuroinflammation associated with Covid-19 that contributed to depression, catatonia, and Cotard’s syndrome. "The most likely diagnosis for this patient is Cotard's Syndrome (also known as walking corpse syndrome), a rare psychological condition where the patient believes they are dead or do not exist. - -Differential diagnoses, ranked by likelihood could include: - -1. Cotard's Syndrome -2. Major Depressive Disorder with Psychotic Features -3. Schizophrenia -4. Dissociative Identity Disorder -5. Bipolar Disorder with Psychotic Features -6. Delusional Disorder -7. Brief Psychotic Disorder -8. Schizoaffective Disorder -9. Complex PTSD -10. Generalized Anxiety Disorder -11. Conversion Disorder -12. Acute Psychotic Disorder due to Covid-19 -13. Substance/Medication-Induced Psychotic Disorder (Steroid Psychosis due to Dexamethasone) -14. Neurocognitive disorder due to vascular illness or other medical condition such as Covid-19 -15. Somatization Disorder." -PMID_35704485-case.txt Unfortunately, diagnosis is often delayed, and patients may be wheelchair-bound or bedbound by the time of diagnosis. The tumor can be found almost anywhere in the body, is usually benign, and can be removed or ablated, although it can recur years later. Tumor-induced osteomalacia is the most likely diagnosis in this patient. I suspect that the diagnostic test was assessment for an elevated blood level of FGF23, followed by imaging studies to identify a tumor. It is prudent to make a biochemical or genetic diagnosis of tumor-induced osteomalacia before performing imaging studies, because the tumor can occur anywhere in the body and false positive imaging studies are common. "Most Likely Diagnoses: Hypophosphatasia (Adult form) - -Differential Diagnosis: - -1. Hypophosphatasia (Adult form) - prominent with consistent fractures and normal calcium and vitamin D levels. -2. Osteomalacia - due to Vitamin D deficiency or metabolism issues. -3. Fibrous Dysplasia - due to occurrence of fractures. -4. Vitamin D-resistant rickets - despite normal Vitamin D levels, it's plausible there may be resistance. -5. Hyperparathyroidism - usually involves raised calcium, but might still be a possibility. -6. Multiple myeloma - repeated fractures could suggest a marrow process like this cancer. -7. Paget's disease of bone - while usually affecting older adults, could potentially cause recurrent fractures. -8. Cushing syndrome - chronic glucocorticoid excess can affect bone health. -9. Osteogenesis imperfecta - a genetic disorder causing brittle bones, although usually diagnosed in childhood. -10. Metastatic cancer - bone metastasis might also cause repeated fractures, although no known primary detected now. -11. McArdle disease - although rare, it can cause muscle weakness leading to frequent fractures. -12. Acromegaly - this results from excess growth hormone and can cause changes in bone structure leading to fractures." -PMID_33730458-case.txt The absence of radiologic evidence of distant metastatic spread indicated early-stage disease, and an extended right hepatectomy with a Roux-en-Y hepaticojejunostomy was performed with curative intent. Pathological examination of the resection specimen revealed an adenocarcinoma that measured 6.5 cm by 6.5 cm by 6.0 cm, with three satellite nodules that ranged from 0.3 cm to 1.4 cm in diameter. Resection margins were negative but close (<1 mm between the cut margin and the tumor), and three lymph nodes were negative for carcinoma. "Most Likely Diagnosis: Intrahepatic cholangiocarcinoma - -Differential Diagnosis: -1. Intrahepatic cholangiocarcinoma -2. Hepatocellular carcinoma -3. Metastatic carcinoma to the liver -4. Hepatic abscess -5. Hepatic adenoma -6. Hepatic sarcoma -7. Focal nodular hyperplasia -8. Hemangioma" -PMID_34525289-case.txt and have relevance to patients presenting for medical care in the context of the current pandemic. The underlying principles are that persons with psychiatric disorders need to be identified and connected with appropriate psychiatric care and that the distress of other members of affected populations is best addressed through psychosocial interventions, such as psychological first aid, without labeling the normative responses to disaster trauma as abnormal. This patient will benefit from observation for the development of a recurrent depressive or anxiety disorder, as well as attention to address her understandable emotional distress. A mental health professional can assess any psychiatric illness that may develop and can assist in the psychosocial aspects of her recovery from her illness through psychotherapeutic interventions including psychosocial support, education, reassurance, and assistance with resumption of her previous level of functioning. In my opinion, this patient is having understandable psychosocial distress in the context of a serious medical illness during the Covid-19 pandemic. The key to understanding this case is to acknowledge that this patient’s distress is a normative response and does not meet criteria for a psychiatric diagnosis. "Most Likely Diagnosis: -1. COVID-19 with acute respiratory distress and psychiatric manifestation in form of acute stress disorder/depressive episode - -Robust Differential Diagnosis (from high to low probability): -1. COVID-19 exacerbated anxiety disorder -2. Influenza with associated anxiety/depressive disorder -3. Community Acquired Pneumonia with psychiatric manifestation -4. COVID-19 induced acute psychosis -5. Viral pneumonia from other sources (Respiratory Syncytial Virus, Parainfluenza Virus etc.) with concurrent psychiatric manifestation -6. Acute stress reaction/psychological distress related to potential life threatening illnesses and suicidal ideation -7. Dehydration and electrolyte imbalance causing mental confusion/stress reaction -8. Serotonin syndrome from overuse of aspirin–paracetamol–caffeine -9. Meningoencephalitis presenting with psychiatric manifestations -10. COVID-19 induced encephalopathy -11. Post-viral fatigue syndrome with psychiatric manifestation -12. Panic disorder with somatic symptoms." -PMID_35731657-case.txt Despite this patient’s young age and inconclusive evaluation, exocrine pancreatic cancer is the most likely cause of the pancreatic mass. This diagnosis is supported by the persistent soft-tissue mass with a double-duct sign (simultaneous dilatation of the biliary and pancreatic ducts), the persistent stricture of the distal bile duct and obstruction of the biliary and pancreatic ducts, the elevated CA 19-9 levels, and the absence of an alternative diagnosis. "Most Likely Diagnosis: Pancreatic ductal adenocarcinoma. - -Differential Diagnosis: -1. Pancreatic ductal adenocarcinoma: The presence of a pancreatic mass coupled with obstructive jaundice, CA 19-9 elevation, and imaging findings suggest this diagnosis. -2. Autoimmune pancreatitis: This could cause the symptomatology and radiological findings, however, a lack of characteristic cellular changes in the aspirate and normal IgG levels make it less likely. -3. Cholangiocarcinoma: Though less likely based on the mass location, it should be considered given the biliary duct dilations and symptoms. -4. Pancreatic neuroendocrine tumor: With a pancreatic mass and symptoms, this is a possibility, but there's no mention of characteristic hormone-related symptoms. -5. Chronic pancreatitis: Recurrent pancreatitis could form a pancreatic mass, however, clinical history doesn't suggest ongoing pancreatitis. -6. Metastatic disease to the pancreas: Less likely given the patient's age and the lack of other systemic symptoms or history of primary malignancy. -7. PanCREatic pseudocyst: Patient history does not suggest recent pancreatitis episode. -8. Ampullary carcinoma: Can cause similar signs and symptoms; less likely given lesion location. -9. Parasitic infection (such as Clonorchis sinensis): Recent sushi consumption and eosinophilia could suggest a parasitic infection causing inflammation and blockage, but would be less common of an explanation for these comprehensive symptoms." -PMID_35584159-case.txt In pulmonary medicine, we have a saying that “everyone aspirates.” Aspiration can be clinically silent and can occur even in the absence of overt reflux symptoms. The centrilobular nodules and tree-in-bud pattern of opacities seen on this patient’s imaging studies are consistent with aspiration. In addition, this patient had secretions in the airways, mucus plugging, a hiatal hernia, and some residual contrast material in the esophagus, all of which are suggestive of aspiration of oral and gastric contents into the airways. His clinical history, especially the history of GERD and a bitter taste in the mouth, suggests the occurrence of aspiration. This patient’s waxing and waning clinical course would also be consistent with aspiration into the airways. The BAL fluid was notable for acute inflammation and the presence of squamous cells, candida, and bacteria, findings that are consistent with — although not specific for — aspiration of oral contents. Given this presentation, additional testing is warranted. On the basis of this patient’s clinical presentation and radiographic evaluation, infectious and aspiration bronchiolitis are the most likely diagnoses in this case. A thorough microbiologic workup was negative except for the fungal markers. The clinical and radiographic presentations are most consistent with a diffuse aspiration bronchiolitis; however, given this patient’s degree of immunosuppression and positive fungal markers, I would proceed with a lung biopsy to rule out fungal pneumonia and to confirm the diagnosis of aspiration bronchiolitis. "Top Diagnosis: Chronic Pulmonary Aspergillosis - -Differential Diagnoses: -1. Chronic Pulmonary Aspergillosis -2. Non-TB Mycobacteria infection -3. Bronchiectasis with secondary bacterial infection -4. Interstitial lung disease -5. Lung abscess -6. Idiopathic Pulmonary Fibrosis -7. COPD with secondary bacterial infection -8. Lung cancer -9. Occupational lung disease (Chronic Hypersensitivity pneumonitis) -10. Pneumonia due to uncommon pathogens such as Nocardia or Actinomyces -11. Rheumatoid Lung Disease -12. Granulomatosis with polyangiitis -13. Pulmonary sarcoidosis -14. Lymphangioleiomyomatosis -15. Langerhans Cell Histiocytosis -" -PMID_36001715-case.txt If specimens obtained during bronchoscopy are nondiagnostic, then lung biopsy by means of video-assisted thoracoscopic surgery should be performed. "Most Likely Diagnosis: Eosinophilic granulomatosis with polyangiitis (EGPA), formerly known as Churg-Strauss syndrome - -Differential Diagnoses (Ranked by Probability): - -1. Eosinophilic granulomatosis with polyangiitis (EGPA) -2. Hypereosinophilic syndrome -3. Granulomatosis with polyangiitis (Wegener's) -4. Pulmonary Langerhans cell histiocytosis -5. Sarcoidosis -6. Metastatic neoplasms -7. Tuberculosis -8. Invasive moles, in the context of the described thyroid and breast nodules -9. Histoplasmosis -10. Hydatid disease, considering the patient’s history of living in Portugal. -" -PMID_35767442-case.txt pected and, in the context of the PET-CT findings, was suggestive of PTLD related to plasmacell myeloma or non-Hodgkin’s lymphoma with associated monoclonal protein. Given the possible diagnosis of PTLD, we elected to proceed with biopsy of a lymph node in the inguinal region, which was the most easily accessible area with lymphadenopathy. "Most Likely Diagnosis: B-Cell Post-Transplantation Lymphoproliferative Disorder (PTLD) - -Differential Diagnosis: -1. B-Cell Post-Transplantation Lymphoproliferative Disorder (PTLD) -2. Graft versus Host Disease (GVHD) with CNS involvement -3. Neurological Manifestation of Acute Lymphoblastic Leukemia -4. Central Nervous System Infection (CNS Infection) -5. Immune Thrombocytopenic Purpura (ITP) -6. Multiple Sclerosis -7. Immune Reconstitution Syndrome -8. Neuromyelitis Optica -9. Vasculitis." -PMID_33567196-case.txt To establish this diagnosis, I would recommend performing a lung biopsy. "Most Likely Diagnosis: Hypersensitivity pneumonitis (HP) with a potential secondary autoimmune disorder - -Differential Diagnosis: -1. Hypersensitivity pneumonitis (HP) -2. Chronic obstructive pulmonary disease (COPD) -3. Bronchiolitis obliterans -4. Pulmonary sarcoidosis -5. Interstitial lung disease related to connective tissue disease -6. Eosinophilic granulomatosis with polyangiitis -7. Occupational lung disease (related to construction site exposure) -8. Asthma with ABPA (Allergic bronchopulmonary aspergillosis) -9. Bronchiectasis -10. Cystic fibrosis (rare for age, but persistent bronchitis raises suspicion) -11. Idiopathic pulmonary fibrosis -12. Non-Tuberculous Mycobacteria (NTM) infection -13. Churg-Strauss syndrome (Eosinophilic Granulomatous Polyangiitis) -14. Pulmonary Langerhans cell histiocytosis -15. Pulmonary alveolar proteinosis -16. Pulmonary vasculitis -17. Severe allergic reaction (e.g. to her asthma medications) -18. Goodpasture Syndrome -19. Lymphangioleiomyomatosis (Rare, but female predominance) -20. Pulmonary embolism (atypical, but could present with dyspnea and normal chest radiograph) -21. Amyloidosis (pulmonary) -22. Pulmonary involvement in IgG4-related disease (Rare and atypical, but high IgE raises slight suspicion) -23. Lung cancer (unlikely with stable nodules and no FDG uptake, but should always be ruled out in a patient with persistent respiratory issues) -24. Gastroesophageal reflux disease-induced respiratory problems -25. Metabolic disease such as alpha-1-antitrypsin deficiency (rare and typically presents in younger individuals) -26. Other rare infections -27. Involutional changes related to aging -28. Cardiac cause of dyspnea like congestive heart failure (unlikely with normal echocardiogram, but keep in mind) -" -PMID_36130001-case.txt Inborn error of immunity. "Most Likely Diagnosis: Autoimmune enteropathy with associated membranous glomerulonephritis - -Differential Diagnoses, ranked by likelihood: - -1. Autoimmune enteropathy with associated membranous glomerulonephritis -2. Celiac disease with secondary nephropathy -3. Intestinal lymphangiectasia with secondary nephropathy -4. Subtle food allergy or malabsorption syndrome -5. Inflammatory bowel disease with secondary renal pathology -6. Immunoglobulin A vasculitis (formerly known as Henoch-Schönlein purpura) -7. Systemic lupus erythematosus with renal and gastrointestinal involvement -8. Immunodeficiency syndromes, like common variable immunodeficiency or selective IgA deficiency with secondary gastrointestinal issues -9. Crohn's disease with associated kidney complications -10. Sarcoidosis with gastrointestinal and renal involvement." -PMID_35172059-case.txt The rapidity of this patient’s disease progression, combined with the known diagnosis of Creutzfeldt–Jakob disease in her father, are highly suggestive of a genetic form of Creutzfeldt–Jakob disease. "Most Likely Diagnosis: Sporadic Creutzfeldt-Jakob disease (sCJD) - -Differential Diagnosis: - -1. Sporadic Creutzfeldt-Jakob disease (sCJD) -2. Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome -3. Progressive multifocal leukoencephalopathy -4. Brainstem encephalitis -5. Wernicke encephalopathy -6. Stiff person syndrome -7. Meningovascular syphilis -8. Anti-GAD antibody syndrome -9. Paraneoplastic syndrome -10. Multisystem atrophy (subtype: MSA-C) -11. Spinocerebellar ataxia -12. Central Pontine Myelinolysis" -PMID_36103417-case.txt GPA is initially responsive to glucocorticoids, but remission requires treatment with either the cytotoxic drug cyclophosphamide or the B-cell– depleting antibody rituximab. Rituximab takes time to work and would not yet have been effective within the 2 weeks after treatment, when this patient’s radiologic findings had progressed and clinical deterioration had occurred. "Most likely diagnosis: IgG4-related disease - -Differential Diagnoses (Ranked from most likely to least likely): -1. IgG4-related disease -2. Giant Cell Arteritis -3. Sarcoidosis -4. Granulomatosis with polyangiitis -5. Takayasu's arteritis -6. Primary angiitis of the central nervous system -7. Neurosarcoidosis -8. Relapsing polychondritis -9. Infection (Bacterial, Viral, or Fungal) -10. Lymphoma -11. Behçet's disease -12. Cryoglobulinemia -13. Systemic lupus erythematosus" -PMID_34379926-case.txt to HIV occurred 3 weeks before hospital admission, the patient would be likely to have a detectable HIV RNA viral load and detectable HIV p24 antigen and may have detectable HIV-1 or HIV-2 antibodies; approximately 30% of patients with acute HIV infection have evidence of an evolving antibody response. "Most Likely Diagnosis: Neurosyphilis - -Differential diagnosis (from most likely to least likely): - -1. Neurosyphilis -2. Acute HIV infection -3. Lyme disease -4. Viral meningitis (e.g., Herpes simplex virus, Enterovirus) -5. Cryptococcal meningitis -6. Tuberculous meningitis -7. Systemic lupus erythematosus with CNS involvement -8. Central nervous system lymphoma -9. Metastatic neoplasm in the central nervous system -10. Toxoplasmosis (brain abscess)" -PMID_35139277-case.txt Diagnostic Testing "The most likely diagnosis: Cogan's Syndrome - -Differential Diagnoses: -1. Cogan's Syndrome -2. Susac's Syndrome -3. Rheumatoid arthritis with secondary Sjögren syndrome -4. Relapsing Polychondritis -5. Wegener's Granulomatosis -6. Neurosyphilis -7. Lyme disease -8. Meniere's disease -9. Sarcoidosis -10. Behçet disease -11. Systemic Lupus Erythematosus -12. Tuberculosis -13. Acute HIV infection -14. Syphilis." -PMID_34161710-case.txt To establish the diagnosis of delayed posthypoxic leukoencephalopathy, I would recommend performing magnetic resonance imaging (MRI) of the head with attention to the T2-weighted fluid-attenuated inversion recovery (FLAIR) sequences. "Most Likely Diagnosis: Central Nervous System Metastasis of Squamous Cell Carcinoma of the Tongue - -Differential Diagnosis: - -1. Central Nervous System Metastasis of Squamous Cell Carcinoma of the Tongue -2. Wernicke's Encephalopathy due to chronic malnutrition and medication -3. Vascular Dementia or Small Vessel Ischemic Disease secondary to radiotherapy -4. Medication-induced Cognitive Impairment or Delirium -5. Chronic Neuropathic Pain Syndrome related Cognitive Impairment -6. Primary Neurodegenerative Disorders such as Alzheimer's Disease -7. Normal Pressure Hydrocephalus -8. Traumatic Brain Injury sequelae exacerbated by cancer treatment stresses -9. Metabolic Encephalopathy. -10. Familial Alzheimer's Disease or other familial neurodegenerative disorders based on family history. -11. Post-radiation Encephalopathy -12. Cerebral Vasculitis or other inflammatory or autoimmune neurological condition. -13. Frontal Lobe Epilepsy or Nonconvulsive Seizure Disorder -14. Brain Abscess or other infectious causes. -15. Subdural Hematoma or other space-occupying lesions. -16. Brain tumor -17. Hypoxic-Ischemic Encephalopathy following cardiac arrest. -18. Psychiatric Disorders such as depression, psychosis or bipolar disorder. -19. Hypothyroidism or other endocrine disorders. -20. Neurosyphilis or other infectious neurologic conditions. -21. ALS/Parkinson's Disease Dementia." -PMID_35045230-case.txt VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome. "Most Likely Diagnosis: -Relapsing polychondritis with progression to systemic vasculitis - -Robust Differential Diagnosis: -1. Relapsing Polychondritis - The patient initially presented with cartilage inflammation that affects the ears, nose, joints, and respiratory tract, which is classic for relapsing polychondritis. -2. Systemic Lupus Erythematosus – It might be possible given the systemic nature of the symptoms, but the patient lacks some common findings such as malar rash, photosensitivity, and positive ANA. -3. Antisynthetase syndrome - This could present with myalgia, but usually involves dysphagia and has a particular rash (mechanic’s hands), none of which the patient has. -4. Granulomatosis with polyangiitis - This could be probable due to the systemic symptoms. However, the patient’s c-ANCA and p-ANCA tests were negative, which would argue against this diagnosis. -5. Polymyalgia rheumatica - The initial diagnosis based on muscle pain and stiffness particularly in the morning in a person over 50 might fit, but the disease progression is not typical of Polymyalgia rheumatica. -6. Rheumatoid Arthritis - Predominantly a joint disease, the systemic effects of Rheumatoid Arthritis could potentially align with some of the symptoms. But the lack of joint degradation and negative factor make it less likely. -7. Giant cell arteritis - This could at first present similarly to polymyalgia rheumatica, the lack of headache, jaw claudication or vision changes makes this diagnosis less likely. -8. Behçet’s disease - Could explain the mucosal ulceration (scleritis), venous thrombosis, and positive pathergy test. However, the patient lacks oral and genital ulcers typically seen in Behçet’s disease. -" -PMID_34788511-case.txt was direct fluorescent antibody staining of an induced-sputum specimen to test for P. jirovecii . "Most Likely Diagnosis: Extrapulmonary sarcoidosis with granulomatous involvement of the liver and salivary gland, and probable sarcoidosis-related pulmonary complications - -Differential Diagnoses: -1. Extrapulmonary sarcoidosis with granulomatous involvement of liver and salivary gland, and sarcoidosis-related lung complications -2. Autoimmune hepatitis -3. Primary biliary cirrhosis -4. Primary sclerosing cholangitis -5. Chronic beryllium disease -6. Lymphoma -7. Tuberculosis -8. Fungal infection, specific histoplasmosis, or cryptococcosis -9. Lymphoproliferative disease associated with autoimmune disease -10. Drug-induced liver disease (possibly related to the methotrexate) -11. Inherited metabolic liver disease -12. Granulomatosis with polyangiitis -13. Hepatic infarction due to thrombosis or embolism -14. Amyloidosis -15. Langerhans' cell histiocytosis." -PMID_36170504-case.txt Alternatively, if surgical resection of the mass is planned, pathological examination of the resection specimen can include an evaluation for islet cells. On the basis of the patient’s presentation with persistent hypoglycemia in the context of a probable sacrococcygeal teratoma, I suspect that the Sotos syndrome is the most likely diagnosis. To establish this diagnosis, targeted sequencing should be performed to identify variants in NSD1 . Alternatively, whole-exome sequencing could be performed in the infant, as well as in the parents if possible (trio approach), to identify pathogenic variants associated with genetic disorders that could be consistent with the patient’s clinical presentation, including the Sotos syndrome. "Most Likely Diagnosis: Sacrococcygeal teratoma with associated persistent hyperinsulinemic hypoglycemia of infancy (PHHI or congenital hyperinsulinism). - -Differential Diagnosis: -1. Sacrococcygeal teratoma with associated persistent hyperinsulinemic hypoglycemia of infancy (PHHI). -2. Neonatal sepsis causing hypoglycemia. -3. Beckwith-Wiedemann Syndrome causing neonatal hypoglycemia. -4. Inborn errors of metabolism causing hypoglycemia, such as glycogen storage disorder. -5. Hypopituitarism-contributing hypoglycemia. -6. Congenital adrenal hyperplasia. -7. Pancreatic beta cell hyperplasia. -8. Dumping syndrome causing hypoglycemia due to rapid gastric emptying." -PMID_34260840-case.txt another cause, listeria infection is the most likely diagnosis in this case. "Most Likely Diagnosis: Septic shock due to unknown source - -Differential Diagnoses: -1. Ectopic pregnancy with rupture -2. Appendicitis -3. Intra-abdominal abscess -4. Pyelonephritis -5. Preeclampsia/HELLP syndrome -6. Pneumonia -7. Drug withdrawal or drug interactions -8. Acute pancreatitis -9. Migraine with aura -10. Placental abruption or placenta previa -11. Influenza or other viral syndromes -12. Systemic lupus erythematosus (SLE) or other connective tissue disorder flare -13. Acute fatty liver of pregnancy -14. Mesenteric ischemia -15. Gastrointestinal bleeding -16. Cushing's syndrome -17. Adrenal insufficiency. -18. Hepatitis or liver disease of acute nature. -19. Hemoglobinopathy complications -20. Mononucleosis and other Epstein Barr Virus (EBV) diseases. -21. Zika virus and other mosquito-borne diseases. -22. Typhoid fever and other salmonella infections." -PMID_36577103-case.txt In this patient with episodic exertional chest discomfort, a flushing syndrome 15 years earlier, and an intracardiac mass, we hypothesized that intratumoral metabolism may have been altered over time and become restricted to dopamine production. With the assistance of a multidisciplinary team of specialists — including specialists in cardiology, interventional cardiology, oncology, radiation oncology, endocrinology, cardiac anesthesia, and cardiac surgery — we developed a plan for perioperative and long-term management. "Most Likely Diagnosis: Coronary Artery Spasm -Differential Diagnosis: -1. Coronary Artery Spasm -2. Hypertrophic Cardiomyopathy -3. Microvascular Angina -4. Vasculitis-induced myocardial ischemia (Eg: Lupus) -5. Premature Coronary Artery Disease -6. Aortic stenosis -7. Above conditions in the presence of physical exertion induced Anaphylaxis -8. Anomalous Origin of the Coronary Artery -9. Variant Angina (Prinzmetal's Angina) -10. Silent Myocardial Ischemia -11. Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC) -12. Spontaneous Coronary Artery Dissection (SCAD) -13. Syndrome X -14. Anxiety/panic disorder leading to palpitations and chest discomfort." -PMID_35196431-case.txt mellitus, acute hyperglycemia with ketosis is a common first presentation; subsequently, betacell destruction leads to absolute insulin deficiency. By contrast, patients with syndromes of insulin resistance and relative insulin deficiency rarely present with ketosis. It is worth noting that this patient, despite his elevated anion gap and serum ketone level, did not have acidemia. However, the venous blood gas analysis and serum bicarbonate level are consistent with an excess of bicarbonate, suggesting that a concurrent metabolic alkalosis (of unclear cause) kept the serum pH in a normal range. In this patient, who had an acute presentation with new hyperglycemia and associated ketosis, autoimmune diabetes is the leading diagnosis. Patients with classic type 1 diabetes mellitus typically first present during childhood or adolescence, and this patient was 68 years of age at symptom onset. Pembrolizumab treatment is his most compelling risk factor for newonset autoimmune diabetes; I suspect that the diagnosis is ICI-induced diabetes. There is no definitive diagnostic test to confirm this diagnosis, but it would be helpful to check blood levels of glycated hemoglobin, islet-cell autoantibodies, and — after treatment with insulin and stabilization of blood glucose levels — C-peptide. "Most Likely Diagnosis: Immunotherapy-induced Type 1 Diabetes Mellitus - -Differential Diagnoses ordered by decreasing probability: - -1. Pembrolizumab-induced Type 1 Diabetes Mellitus (rapid onset) -2. Steroid-induced hyperglycemia (though use not mentioned in the case) -3. Stress Hyperglycemia (related to Metastatic Melanoma) -4. Latent Autoimmune Diabetes in Adults (LADA) -5. Pancreatic malignancy-related Diabetes Mellitus (metastasis from melanoma unlikely but possible) -6. Type 2 Diabetes Mellitus (less likely given rapid onset and severe hyperglycemia) -7. Cushing's Syndrome (no mention of typical phenotypic features, only hyperglycemia) -8. Drug induced hyperglycemia secondary to other medications (less likely)." -PMID_35081284-case.txt Children with IBD often “fall off” the growth curve long before the diagnosis is made. An early sign of growth failure is a decrease in height velocity. The most likely diagnosis in this patient is IBD. His initial vague gastrointestinal symptoms are atypical of this condition; however, arthralgias and oral aphthous ulcers are both common extraintestinal manifestations. He did not have frankly bloody stools, which could explain why the hemoglobin level was only mildly decreased. The decreased albumin level and mildly elevated lipase level are consistent with a diagnosis of IBD, and the elevated levels of inflammatory markers support the diagnosis. Several features of this patient’s presentation give me pause. Presentation with arthralgias as the dominant symptom and with only mild gastrointestinal symptoms is highly unusual, as is the fact that the most affected joint was his shoulder. Also, he did not have a history of weight loss or growth failure; the absence of these features suggests a recent and rapid onset of illness. Despite his somewhat unusual presentation, I think IBD is the most likely diagnosis in this case. To establish this diagnosis, I would perform colonoscopy and upper endoscopy. "Most likely diagnosis: Lyme disease - -Differential diagnosis, ranked from most likely to least likely: -1. Lyme disease -2. Infectious mononucleosis -3. Juvenile rheumatoid arthritis -4. Leukemia -5. RMSF (Rocky Mountain spotted fever) -6. Anaplasmosis/Ehrlichiosis -7. Septic arthritis -8. Gastroenteritis -9. Sarcoidosis -10. Crohn's disease" -PMID_34879452-case.txt Approximately 50% of cases are associated with oral ulcers, often on the tongue. The arthralgias, fever, presence of anti-Ro antibodies, abnormal results on liverfunction tests, and elevated ferritin level seen in this patient are common in patients with anti– MDA-5 dermatomyositis. I suspect that the most likely diagnosis in this patient is anti–MDA-5 dermatomyositis. To establish this diagnosis, I would review the results of the muscle biopsy and test for antibodies directed against myositis-associated autoantigens, including MDA-5. "Most likely diagnosis: Still's disease, Adult-Onset - -Differential Diagnosis (beginning with most likely): -1. Still's disease, Adult-Onset -2. Disseminated Gonococcal infection -3. SLE (Systemic Lupus Erythematosus) -4. Polymyositis -5. Rheumatoid arthritis -6. Coccidioidomycosis -7. Histoplasmosis -8. Leptospirosis -9. Hemochromatosis -10. Bacterial endocarditis -11. Behçet's disease -12. Mycobacterial infection (Mycobacterium tuberculosis) -13. Dermatomyositis -14. Mixed connective tissue disease (MCTD) -15. Reactive arthritis -16. Sjögren's Syndrome -17. Candidiasis involving the oral cavity (thrush) -18. Paraneoplastic syndrome associated with hidden malignancy -19. Neuroendocrine tumour (related to adrenal nodule)" -PMID_34706175-case.txt Although this patient did not have evidence of leukemic cells on oral biopsy, the diagnosis of leukemia would account for his weight loss, worsening ulcers that did not respond to therapy, and increasing eosinophilia despite treatment with glucocorticoids. To establish the diagnosis in this case, I would recommend a bone marrow biopsy. "Most likely diagnosis: Behçet's disease, given the presence of painful oral ulcers, eye involvement, positive HLA-B51 allele, and consideration of this diagnosis already made by the rheumatology and dermatology services that initiated treatment with colchicine. - -Differential diagnosis, in decreasing order of likelihood: - -1. Behçet's disease -2. Mucous membrane pemphigoid: Given the oral lesions and suspected esophageal involvement causing weight loss, but negative antibody tests make this less likely. -3. Crohn’s disease: Oral ulcers could be an extra-intestinal manifestation of Crohn’s disease, with weight loss suggesting possible gastrointestinal involvement. -4. Herpes simplex virus infection: Although the patient was tested negative, this could still be a possibility due to atypical presentation or limitations of testing. -5. Autoimmune blistering diseases (like pemphigus vulgaris): Though negative antibody test results make these less likely. -6. MAGIC syndrome (Mouth and Genital ulcers with Inflamed Cartilage): No genital ulcers or cartilage inflammation is present, but this could still be a consideration. -7. Cicatricial pemphigoid: This could cause mouth ulcers, though other typical features are absent. -8. Lymphoma: The presence of prominent lymph nodes in the CT scan raises a possible malignancy like lymphoma which can manifest with systemic symptoms like weight loss. -9. Squamous cell carcinoma: This could present with oral ulcers and weight loss, but biopsy results do not support this diagnosis. -10. Tuberculosis: This can sometimes present with ulcers and weight loss, and endemic areas were visited by the patient. However, lung involvement is not typical, and no other signs of infection are present. -11. Gastroesophageal reflux disease (GERD): The patient has a medical history of GERD, which could cause weight loss due to difficulty swallowing, but it would not explain the oral ulcers." -PMID_35443111-case.txt Systemic lupus erythematosus. "Most Likely Diagnosis: Systemic Lupus Erythematosus (SLE) with associated Libman-Sacks endocarditis. - -Differential Diagnosis: -1. Systemic Lupus Erythematosus (SLE) with associated Libman-Sacks endocarditis. -2. Primary Antiphospholipid Syndrome with associated cardiac vegetations. -3. Bacterial endocarditis. -4. Non-infectious thrombotic endocarditis (marantic endocarditis) associated with malignancy. -5. Hypercoagulable state due to underlying malignancy leading to cardiac vegetations. -6. Thrombotic thrombocytopenic purpura (TTP) or other microangiopathic haemolytic anemia. -7. Mitral valve prolapse with associated myxomatous degeneration and secondary thrombus formation. -8. Rare infectious causes of endocarditis (e.g., fungal, Q fever). -9. Rheumatoid arthritis with cardiac involvement. -10. Primary cardiac tumor such as myxoma." -PMID_36260795-case.txt Drug reaction with eosinophilia and systemic symptoms complicated by eosinophilic myocarditis. "Most likely diagnosis: -Infective Endocarditis (IE) due to Methicillin-Sensitive Staphylococcus Aureus (MSSA) - -Differential Diagnoses: -1. MSSA Septicemia -2. Congestive Heart Failure due to Valvular Heart Disease -3. Septic Emboli -4. Atrial Fibrillation related complications -5. Right Heart Failure due to Severe Tricuspid Regurgitation -6. Left Heart Failure due to Mitral Regurgitation -7. Drug-induced hypersensitivity syndrome -8. End-Organ Damage due to MSSA Bacteremia -9. Postoperative complications including Ventricular tachycardia, Deep vein thrombosis, and kidney dysfunction -10. Post-cardiotomy syndrome -11. Anaphylactoid purpura -12. Bacteremia-induced vasoplegia -13. Chronic prosthetic valve dysfunction -14. Complications from coronary artery disease and its treatment -15. Hypothyroidism contributing to heart failure -16. Hypersensitivity-related systemic inflammatory response syndrome -17. Right Coronary Artery Stenosis -18. Prosthetic valve Endocarditis -19. Staphylococcal toxic shock syndrome -20. Acute respiratory distress syndrome secondary to fluid overload." -PMID_34320292-case.txt Dr. Olivia C. Smibert’s Diagnosis "Most likely diagnoses: Thrombotic Thrombocytopenic Purpura (TTP) triggered by calcineurin inhibitor toxicity. - -Differential Diagnoses: -1. Thrombotic Thrombocytopenic Purpura (TTP) -2. Hemolytic Uremic Syndrome (HUS) -3. Drug-induced thrombocytopenia -4. Disseminated Intravascular Coagulation (DIC) -5. Immune Thrombocytopenic Purpura (ITP) -6. Paroxysmal nocturnal hemoglobinuria -7. Severe aplastic anemia -8. Post-transplant lymphoproliferative disease -9. Acute graft rejection -10. Virally induced thrombocytopenia (such as due to CMV or EBV). -11. Anti-phospholipid syndrome" -PMID_34107184-case.txt Acquired clotting-factor inhibitor. "Most Likely Diagnosis: -Spontaneous hematoma secondary to anticoagulant use (aspirin), likely exacerbated by underlying vascular disease. - -Differential Diagnosis: -- Anticoagulant-Related Hematoma -- Atraumatic Rupture of Vascular Tumor -- Hemophilia -- Vascular Malformation Bleeding -- Intramuscular Hemangioma with Spontaneous Rupture -- Acute Compartment Syndrome due to Hematoma -- Spontaneous Bleeding from a Coagulation Factor Deficiency (e.g., Von Willebrand Disease) -- Bleeding Secondary to Drug-Induced Thrombocytopenia -- Disseminated Intravascular Coagulation -- Hematoma secondary to myositis ossificans -- Aneurysmal Rupture" -PMID_35476654-case.txt Although endomyocardial biopsy may confirm the diagnosis of myocarditis caused by L. monocytogenes , the risks associated with biopsy were thought to outweigh the benefits, so microbial cell-free DNA sequencing was recommended as an alternative diagnostic test. "Most Likely Diagnosis: Lyme carditis - -Differential Diagnoses Ranked: - -1. Lyme Carditis -2. Giant cell arteritis -3. Polymyalgia rheumatica -4. Bacterial Endocarditis -5. Myocarditis secondary to autoimmune disease (Systemic Lupus Erythematosus, Rheumatoid arthritis) -6. Fibromyalgia -7. Serum sickness-like reaction -8. Bacterial myocarditis -9. Parasitic myocarditis (Toxoplasma, Chagas) -10. Tuberculosis pericarditis or myocarditis -11. Viral myocarditis (Influenza, Epstein-Barr, Syndrome of the acute respiratory, Hepatitis C) -12. Endocrine disorders (hypothyroidism, adrenal insufficiency) -13. Hemochromatosis or other metabolic storage diseases. -14. Paraneoplastic syndromes." -PMID_36477035-case.txt In this patient who had no risk factors for tuberculosis, the clinical syndrome of a progressive, fulminant illness with fever, innumerable pulmonary nodules, splenomegaly, and hypercalcemia occurring 7 months after kidney transplantation is most likely due to donor-derived infection with M. tuberculosis . Some patients may have risk factors for tuberculosis that are not identified initially, and once such risk factors are identified, a thorough requestioning of the patient is needed. To establish a diagnosis of tuberculosis, I would obtain pulmonary specimens for an acid-fast bacilli smear, nucleic acid amplification testing, and culture. I would begin the investigation by obtaining an induced sputum sample but would rapidly pursue bronchoscopy and biopsy of a pulmonary nodule if acid-fast staining and nucleic acid amplification testing are negative. I would evaluate concurrently for several of the diagnoses discussed previously, given the critical nature of this patient’s presentation and the possibility that an immunocompromised host may have multiple coexisting diseases at the time of presentation. "Most Likely Diagnosis: -Post-transplant lymphoproliferative disorder (PTLD) associated with Epstein-Barr Virus (EBV) infection. - -Differential Diagnosis (ranked from most likely to least likely): -1. Post-transplant lymphoproliferative disorder (PTLD) associated with Epstein-Barr Virus (EBV) infection. -2. Cytomegalovirus (CMV) infection. -3. Diffuse alveolar hemorrhage due to immunosuppression. -4. Sepsis due to bacterial or mycobacterial infection. -5. Fungal infection such as invasive aspergillosis, particularly in the context of recent immunosuppression modification. -6. Sarcoidosis reactivation. -7. Kidney transplant rejection with systemic complications. -8. Hemophagocytic lymphohistiocytosis (HLH). -9. Pneumocystis jirovecii pneumonia. -10. Pulmonary embolism. -11. Lymphoma. -12. Paraneoplastic syndrome associated with unknown malignancy." -PMID_35417641-case.txt For this reason, I think that the schistocytes are a “red herring” in this case that biased the initial diagnosis toward a destructive process such as TTP, rather than a production problem such as MDS. Overall, this patient’s history and current presentation are consistent with progression of MDS. I suspect that the diagnostic test was a repeat bone marrow biopsy with cytogenetic analysis and next-generation sequencing. "Most likely diagnosis: Hemophagocytic lymphohistiocytosis (HLH) secondary to Candida esophagitis - -Differential Diagnosis: -1. Hemophagocytic lymphohistiocytosis (HLH) secondary to Candida esophagitis -2. Thrombotic Thrombocytopenic Purpura (TTP) -3. Autoimmune Hemolytic Anemia with Evans Syndrome -4. Disseminated Intravascular Coagulation (DIC) -5. Paroxysmal Nocturnal Hemoglobinuria (PNH) -6. Antiphospholipid Syndrome (APS) -7. Myelodysplastic Syndrome (MDS) -8. B12 or Folate Deficiency Anemia -9. Acute leukemia -10. Multiple Myeloma -11. Sepsis secondary to Candida esophagitis -12. Hepatic Disease -13. Pancytopenia secondary to marrow infiltration by metastatic cancer (due to presence of bilateral adnexal lesions) -14. Drug-induced hemolysis or thrombocytopenia due to amlodipine, atorvastatin or hydrochlorothiazide." -PMID_33497551-case.txt The patient could have primary disseminated tuberculosis, but she is more likely to have reactivation of largely latent disseminated disease in the pleura and CNS as a result of progressive chronic kidney disease, diabetes mellitus, age, and reduced gastric acidity due to gastrectomy. "Most Likely Diagnosis: Paraneoplastic limbic encephalitis associated with gastric adenocarcinoma. - -Differential Diagnoses: -1. Paraneoplastic limbic encephalitis associated with gastric adenocarcinoma -2. Cerebral vasculitis -3. Neurosyphilis -4. Intracranial metastasis -5. Cerebral toxoplasmosis -6. Central nervous system lymphoma -7. Progressive multifocal leukoencephalopathy -8. Cerebral abscess -9. Tuberculous meningitis -10. Neurocysticercosis -11. Cerebral amoebiasis -12. Acute disseminated encephalomyelitis (ADEM) -13. Neurosarcoidosis -14. Inflammatory CNS demyelination (MS variant) -15. Cerebral Whipple's disease -16. Fungal meningitis (Cryptococcus, Coccidioides, Histoplasma) -17. Listeria rhombencephalitis -18. Subacute sclerosing panencephalitis (SSPE) -19. Paraneoplastic cerebellar degeneration." -PMID_34551232-case.txt performed to obtain a more sensitive view of the joints and to rule out occult osteomyelitis and tumor. The presence of widespread lymphadenopathy on MRI would further support the diagnosis of systemic juvenile idiopathic arthritis. If arthritis were absent but more accessible lymph nodes were identified, diagnostic biopsy would have been considered. "Most Likely Diagnosis: Juvenile rheumatoid arthritis or Still's disease - -Differential Diagnoses, in order from most likely to least likely: - -1. Juvenile rheumatoid arthritis or Still's disease -2. Kawasaki disease -3. Hemophagocytic lymphohistiocytosis (HLH) -4. Leukemia or other malignancy -5. Juvenile systemic lupus erythematosus -6. Infective Endocarditis -7. Sepsis -8. Acute Hepatitis -9. Acute Rheumatic Fever -10. Lyme disease -11. Mevalonate kinase deficiency (Hyper IgD syndrome) -12. Vasculitis, potentially Henoch-Schönlein purpura -13. Dermatomyositis -14. Familial Mediterranean fever." -PMID_35675180-case.txt mixed connective-tissue disease. I would recommend further evaluation, including testing for anti–U1-ribonucleoprotein (RNP) antibodies and antinuclear antibodies (ANA), cardiac magnetic resonance imaging (MRI), and renovascular imaging. "Most likely diagnosis: Myocarditis - -Differential diagnoses, from most likely to least likely: - -1. Myocarditis -2. Pericarditis -3. Coronary artery disease -4. Pulmonary embolism -5. Viral infection such as Coxsackievirus B -6. Hypertrophic cardiomyopathy -7. Systemic lupus erythematosus (SLE) -8. Rheumatic heart disease -9. Lyme carditis -10. Kawasaki disease -11. Takotsubo cardiomyopathy -12. Infective endocarditis -13. Sarcoidosis -14. Anemia -15. Constrictive pericarditis -16. Thalassemia -17. Polycythemia vera -18. Hyponatremia -19. Hyperkalemia -20. Addison's disease -21. Diabetic ketoacidosis -22. Hypothyroidism -23. Hyperthyroidism -24. Atrial fibrillation -25. Pheochromocytoma -26. Anorexia nervosa -27. Familial Mediterranean fever -28. Juvenile idiopathic arthritis -29. Hemochromatosis -30. Glycogen storage diseases -31. Mitochondrial diseases -32. Cystic fibrosis -33. Hemolytic-uremic syndrome -34. Barth syndrome -35. Familial hypercholesterolemia." -PMID_33704941-case.txt and neurologic findings, we suspected that the trigger was meningococcal disease. "The most likely diagnosis for this case is Streptococcal Toxic Shock Syndrome (STSS) due to group A Streptococcus. - -Differential diagnosis, starting from most likely to least likely: - -1. Streptococcal Toxic Shock Syndrome (STSS) -2. Necrotizing fasciitis -3. Microscopic polyangiitis -4. Septic shock from a different bacterial infection, such as staphylococcus or a gram negative organism -5. Hemorrhagic fever viruses -6. Toxic epidermal necrolysis/Stevens-Johnson syndrome -7. Meningococcemia -8. Rocky mountain spotted fever -9. Bacterial septicemia -10. Disseminated intravascular coagulation -11. Leptospirosis -12. Dengue fever -13. Kawasaki disease -14. Hantavirus pulmonary syndrome -15. Drug-induced vasculitis -16. Catastrophic antiphospholipid syndrome." -PMID_35263523-case.txt I recommended repeat MRI of the head with the administration of gadolinium as the next step in the evaluation of this patient. "Most likely diagnosis: Creutzfeldt-Jakob disease (CJD) - -Differential Diagnosis: -1. Creutzfeldt-Jakob disease (CJD) -2. Major depressive disorder -3. Conversion disorder -4. Progressive multifocal leukoencephalopathy -5. Alzheimer's disease -6. Normal pressure hydrocephalus -7. Multiple sclerosis -8. Psychogenic non-epileptic seizures -9. vascular dementia -10. Parkinson's disease -11. Frontotemporal dementia -12. Glioma -13. Wernicke-Korsakoff syndrome -14. Chronic Traumatic Encephalopathy -15. Lewy body dementia" -PMID_34758256-case.txt On the basis of the features of the patient’s presentation, the fact that he had been healthy the day before the seizure, and his history of living in a rural area of Guatemala, neurocysticercosis is the most likely diagnosis in this case. To establish this diagnosis, CT was most likely performed, followed by MRI and EEG. "Most likely diagnosis: Neurocysticercosis. - -Differential Diagnosis (ranked by probability): - -1. Neurocysticercosis: Given the patient's immigration history from rural Guatemala, where this parasitic infection is endemic, this could be the cause of his reported seizures and altered mental status. - -2. Encephalitis: This could be due to a viral, bacterial, or parasitic infection and could cause seizures and altered mental status. - -3. Meningitis: This can cause an altered level of consciousness and seizures, but the absence of fever and neck stiffness makes it less likely in this case. - -4. Brain tumor: Could cause seizures and an altered mental status, but this is less likely given the patient's relatively young age and the absence of other neurological symptoms. - -5. Subarachnoid hemorrhage: This could present with seizures and an altered mental state. However, the lack of a headache or vomiting makes it less likely. - -6. Epileptic seizures: Given the history of a first tonic-clonic seizure, primary epilepsy may be a possibility. However, given the dramatic presentation and lack of personal or family history of epilepsy, this would be a less likely diagnosis. - -7. Drug or Alcohol Withdrawal: Despite the patient reporting limited alcohol and no illicit drug use, withdrawal could potentially lead to seizures and altered mental status. - -8. Cerebral Vasculitis: This is a rare condition but could cause seizures and altered mental status due to inflammation and damage to brain tissue. - -9. Metabolic disturbances: Hypoglycemia, hyponatremia, hypocalcemia or any significant electrolyte imbalance could lead to neurological signs. However, given the normal blood glucose level, this seems unlikely. - -10. Psychogenic Non-Epileptic Seizures (PNES): These are seizure-like episodes that are psychological, not neurological, in nature. The episodes tend to be less predictable than epileptic seizures and may resemble a variety of neurological disorders." -PMID_33761211-case.txt -adrenergic receptors decrease insulin release and can cause hyperglycemia. Taken together, all the features suggest that the most likely diagnosis in this patient is pheochromocytoma. The first step in establishing this diagnosis is to perform abdominal imaging to look for an adrenal tumor consistent with pheochromocytoma. "Most Likely Diagnosis: Pheochromocytoma - -Differential Diagnosis (from most to least likely): -1. Pheochromocytoma – This sets off the symptoms of migraine headaches, hypertension, and increased hormonal secretion. -2. Autonomic Dysreflexia – After his ATV accident, a spinal cord injury could potentially cause this condition which includes extremely high blood pressure. -3. Cushing’s Syndrome/Disease – His headaches, high blood pressure, abdominal pain, and other symptoms align with this disease. -4. Adrenal Insufficiency (due to Addison's disease or secondary causes) – While less likely, adrenal problems could potentially cause these symptoms. -5. Neuroblastoma – Though most common in younger children, this cancer could possibly cause his symptoms. -6. Giant Cell Arteritis – It could cause severe headaches and is related to systemic inflammation. -7. Malignant Hypertension – It could cause headaches and high blood pressure, although it is unlikely given his age. -8. Intracranial Hypertension – The headaches and vomiting could be symptomatic of this, but it does not explain the high blood pressure. -9. Primary aldosteronism – Hormonal issues from the adrenal gland could theoretically cause these symptoms." -PMID_33852783-case.txt In summary, this patient’s presentation with regional tender lymphadenopathy and history of exposure to cats makes cat scratch disease the most likely diagnosis in this case. An atypical presentation of a systemic infection, a systemic granulomatous process such as sarcoidosis, and lymphoproliferative disorder cannot be ruled out. To establish the diagnosis, I would recommend a right inguinal lymph-node biopsy and serologic testing for B. henselae and other infectious causes. "Most Likely Diagnosis: Bacteremia secondary to urinary tract infection (UTI) caused by Escherichia coli and Klebsiella pneumoniae - -Differential Diagnosis: -1. Bacteremia secondary to UTI - E. coli & K. pneumoniae -2. Acute Pyelonephritis, feasibly due to E. coli or K. pneumoniae -3. Lymphogranuloma venereum or Cat-scratch disease - Due to the bilateral inguinal lymphadenopathy -4. Tuberculous pelvic inflammatory disease - History of contact with an aunt who had tuberculosis -5. Bacterial endocarditis - Given the persistent fever and history of UTI -6. Pelvic inflammatory disease - Considering the lower abdominal pain and history of inserting an IUD -7. Lymphoma - Given the presence of multiple sites of lymphadenopathy -8. Appendicitis - Given flank pain, right side abdominal tenderness, and fever -9. Tumors metastases - Considering her multiple enlarged lymph nodes and persistent weight loss -10. Leukemia - Taking into account her persistent fever, lymphadenopathy, and leukocytosis. -11. Toxoplasmosis - Considering her contact with cats and lymphadenopathy." -PMID_36239648-case.txt both gastric accommodation and gastric emptying. Progressive disease can lead to gastric-outlet obstruction. Because the liver is the common venous drainage point for most of the gastrointestinal tract, it is a frequent site of hematogenous metastases, which appear as hypodense lesions on CT. This patient initially had breakthrough heartburn that did not respond to previously effective acid-suppression therapy, which could represent malignant infiltration of the clasplike sling fibers that originate from the upper stomach and form part of the normal acid barrier. Malignant infiltration of the submucosal and muscularis propria layers of the fundus impairs normal gastric accommodation, which leads to early satiation. Malignant infiltration of the entire antral wall disrupts the neurocircuitry and muscular contractions that are required for gastric emptying. This process initially mimics gastroparesis, with retention of solid food and nausea, but prokinetic treatments are ineffective because damage to the muscularis propria prevents these agents from effectively triggering antral contractions. Liquids are initially tolerated because they are emptied passively. However, progressive antral disease marks a transition from gastroparesis to gastric-outlet obstruction, and liquids are no longer tolerated. Patients with linitis plastica frequently present with advanced disease, and this patient’s hypodense liver lesions may suggest metastatic disease. Given this patient’s rapidly progressive symptoms that are suggestive of specific alterations in gastric physiology, in combination with his imaging and EGD findings, I favor a diagnosis of gastric cancer that is consistent with linitis plastica. The diagnostic test of choice would be endoscopic ultrasonography (EUS). "Most Likely Diagnosis: -Gastrointestinal stromal tumor (GIST) with metastatic spread to the liver and lungs. - -Differential Diagnoses Ranked by Probability: - -1. Gastrointestinal stromal tumor (GIST) with metastatic spread to liver and lungs. -2. Gastric adenocarcinoma with metastatic spread to liver and lungs. -3. Diffuse gastric carcinoma (linitis plastica) with metastasis. -4. Gastric lymphoma with metastatic disease. -5. Metastatic pancreatic cancer with gastric involvement. -6. Gastric sarcoma with metastasis. -7. Systemic disease like systemic sclerosis (scleroderma) causing gastric and esophageal dysmotility. -8. Neuroendocrine tumor with primary in the stomach or pancreas causing paraneoplastic motility disorder in the stomach. -9. Submucosal infiltration due to any connective tissue disease with malignancy. -10. Peptic ulcer disease with pyloric stenosis (though unlikely given the CT findings of wall thickening and presence of pulmonary and hepatic lesions)." -PMID_33626257-case.txt Identification of high-grade lymphoma is an unlikely but plausible result. "Most Likely Diagnosis: Waldenström’s macroglobulinemia with Central Nervous System (CNS) involvement causing optic neuropathy - -Differential Diagnoses: - -1. Waldenström’s macroglobulinemia with CNS involvement causing optic neuropathy - -2. IgM monoclonal gammopathy of undetermined significance (MGUS) with optic neuropathy - -3. Intracranial lesion (e.g., meningioma, metastasis) compressing the optic nerve - -4. Infiltrative ophthalmopathy secondary to lymphoma - -5. Temporal (Giant cell) arteritis with vision loss - -6. Cryptococcal meningitis causing increased intracranial pressure and subsequent optic neuropathy - -7. Optic neuritis secondary to autoimmune disease (Multiple sclerosis, Sjogren’s syndrome) - -8. Ischemic optic neuropathy (anterior or posterior) - -9. Intracranial mass effect (due to neoplasm or abscess) - -10. Leber's Hereditary Optic Neuropathy (LHON) - -11. Neurosyphilis (including tabes dorsalis) - -12. Neurological sequelae secondary to Lyme disease - -13. Toxoplasmosis retinochoroiditis - -The most likely diagnosis is at the top with the least likely at the bottom. The listed conditions could present with visual symptoms and are ranked according to this specific patient’s history, examination findings, and lab results. " -PMID_33503346-case.txt If the diagnosis of primary amyloidosis is confirmed in this patient, I would also recommend a bone marrow biopsy to rule out multiple myeloma, which occurs in 10 to 15% of patients with primary amyloidosis. "Most Likely Diagnoses: Sarcoidosis - -Differential Diagnosis: - -1. Sarcoidosis -2. Giant Cell Arteritis: The patient's age (over 50), jaw claudication, temporal headache, and elevated ESR places this in the differential. -3. Orbital Tumour: Possible due to the palpable irregular mass under the patient's left superior orbital rim. -4. Intracranial mass or aneurysm -5. Ophthalmic Artery Occlusion -6. Temporal Arteritis: The age, bilateral temporal artery prominence, recent temporal headache, and loss of vision make this disorder a possibility. -7. Dermatomyositis: Elevated muscle enzymes, fatigue, and weight loss may be pointing to this diagnosis. -8. Polymyalgia rheumatica: Jaw claudication and hip pain after walking could imply polymyalgia rheumatica. -9. Primary Biliary Cirrhosis: Elevated liver function tests and alkaline phosphatase might point to this diagnosis. -10. Amyloidosis: Systemic symptoms along with kidney and liver involvement can suggest this. -11. Hepatitis B or C: Aspartate Aminotransferase, Alanine Aminotransferase, and alkaline phosphatase were all elevated. -12. Primary or Metastatic Liver Cancer are also possibilities given the liver parenchyma heterogeneity and periportal lymph node enlargement identified on ultrasonography. -13. Rare Infections such as tuberculosis or fungal infection: Given the patient's extensive travel history and globetrotting lifestyle, it is possible that he may have contracted a classical or an opportunistic infection." -PMID_34936743-case.txt but the history does not suggest such an exposure. Because fat droplets are compliant enough to pass through the pulmonary capillary bed and embolize to the central nervous system even in the absence of a patent foramen ovale, the diagnosis of fat embolism syndrome occurring after the liposuction procedure best explains this patient’s combination of lung injury, diffuse alveolar hemorrhage, and cerebral injury. "Most Likely Diagnosis: Fat Embolism Syndrome (FES) - -Differential Diagnoses: - -1. Fat Embolism Syndrome (FES) -2. Diffuse Alveolar Hemorrhage (DAH) -3. Severe Acute Respiratory Syndrome (SARS) -4. Eosinophilic Pneumonia -5. Pulmonary Hemorrhage due to Vasculitis -6. Severe COVID-19-induced pneumonia -7. Pulmonary Edema secondary to acute heart failure -8. Acute Interstitial Pneumonia (AIP) -9. Acute Respiratory Distress Syndrome (ARDS) -10. Pulmonary Embolism -11. Aspiration Pneumonia -12. Drug-induced Toxicity (Antibiotics or Opiates) causing Pneumonitis -13. Pulmonary Contusion -14. Acute Pancreatitis leading to ARDS -15. Trauma prompting Pulmonary Parenchymal Injury." -PMID_34437787-case.txt splice acceptor variant was present at both the time of initial diagnosis and the time of relapse; this pattern is consistent with that observed in these similar cases. "First Piece of Information - Most likely diagnosis: -Relapse of Acute Myeloid Leukemia (AML) with mutated NPM1 - -Second Piece of Information - Differential Diagnosis (from most likely to least likely): - -1. Relapse of Acute Myeloid Leukemia (AML) with mutated NPM1 -2. Myelodysplastic syndrome (MDS) -3. Chronic Myelomonocytic Leukemia (CMML) -4. Acute Lymphoblastic Leukemia (ALL) -5. Transformation of a previously undiagnosed Myeloproliferative Neoplasm (MPN) into Acute Myeloid Leukemia (AML) -6. Paroxysmal Nocturnal Hemoglobinuria (PNH) with secondary AML -7. Secondary AML after chemotherapy (therapy-related AML) -8. Hemophagocytic Lymphohistiocytosis (HLH) -9. Aplastic anemia with dysplasia or transformation to AML -10. Idiopathic Hypereosinophilic Syndrome (HES) with transformation to AML." -PMID_35939582-case.txt tory, and duration of symptoms are most consistent with a diagnosis of insulinoma. To establish this diagnosis, I would initiate a supervised fast to monitor for symptomatic hypoglycemia. In addition, I would measure serum levels of glucose, insulin, C-peptide, proinsulin, and β-hydroxybutyrate. "Most likely diagnosis: Insulinoma - -Differential Diagnoses: - -1. Insulinoma -2. Factitious hypoglycemia -3. Non-insulinoma pancreatogenous hypoglycemia syndrome (NIPHS) -4. Reactive hypoglycemia -5. Addison's disease -6. Severe liver disease -7. Insulin autoimmune syndrome (Hirata disease) -8. Inherited metabolic disorders (Rare in adults) -9. Post gastric bypass hypoglycemia -10. Adrenal insufficiency" -PMID_33979492-case.txt Hemophagocytic lymphohistiocytosis. "Most Likely Diagnoses: Hemophagocytic lymphohistiocytosis - -Differential Diagnoses: -1. Hemophagocytic lymphohistiocytosis (HLH) -2. Paroxysmal nocturnal hemoglobinuria (PNH) -3. Myelodysplastic syndrome -4. Chronic lymphocytic leukemia (CLL) -5. Autoimmune lymphoproliferative syndrome (ALPS) -6. Systemic lupus erythematosus (SLE) -7. Leukemia, in particular acute lymphoblastic leukemia -8. Lymphoma, in particular non-Hodgkin lymphoma -9. Malaria -10. Cholecystitis due to the noted cholelithiasis -11. Symptoms related to known Multiple Sclerosis -12. Epstein-Barr virus (EBV) or other viral infection, such as cytomegalovirus (CMV) -13. Granulomatous disease, especially sarcoidosis -14. Lymphoproliferative disorder due to immunosuppression. -15. Spleen infection or abscess -16. Hepatosplenic T-cell lymphoma" -PMID_35294816-case.txt of C4, C1 inhibitor, and C1q, as well as a repeat assessment of C1 inhibitor function, to further investigate her previous diagnosis of acquired C1 inhibitor deficiency and the possibility of a diagnosis of hereditary angioedema with C1 inhibitor deficiency. "Most Likely Diagnosis: Acquired angioedema due to C1 inhibitor deficiency. - -Differential Diagnosis: - -1. Acquired angioedema due to C1 inhibitor deficiency -2. Hereditary angioedema with normal C1 inhibitor level and function -3. Acquired angioedema due to C1 inhibitor deficiency secondary to malignancy -4. Systemic lupus erythematosus -5. Auriculotemporal syndrome -6. Cryoglobulinemia -7. Urticarial vasculitis -8. Pellagra or niacin deficiency -9. Distal renal tubular acidosis -10. Hypocomplementemic urticarial vasculitis -11. Acute allergic reaction, chronic idiopathic urticaria -12. Hypersensitivity reaction to NSAIDS -13. Episodic angioedema with eosinophilia (Gleich's syndrome)" -PMID_34407347-case.txt Systemic iron-overload syndrome. "Based on the evidence provided, my most likely diagnosis is Decompensated Alcoholic Liver Disease (cirrhosis), precipitated by the patient's long history of alcohol consumption and his associated clinical findings including edema, ascites, coarsened liver texture on ultrasound, and a history of decreased albumin. - -A differential diagnosis, in descending order of likelihood, includes: - -1. Decompensated Alcoholic Liver Disease/Cirrhosis -2. Alcoholic Hepatitis -3. Non-alcoholic Steatohepatitis (NASH) -4. Heart Failure -5. Chronic Kidney Disease -6. Diabetes with severe insulin resistance -7. Panhypopituitarism -8. Hypothyroidism" -PMID_34587390-case.txt The findings on echocardiography in this case ruled out aneurysm involving the ascending aorta or aortic root. In view of all these factors and the overall frequency at which these mutations arise in the population, the most likely genetic diagnosis in this patient, who had recurrent dissection of medium-sized arteries and joint dysfunction in the absence of thoracic aortic aneurysm, is the vascular form of Ehlers–Danlos syndrome, which is caused by mutations in COL3A1 . "Most Likely Diagnosis: Fibromuscular dysplasia - -Differential Diagnoses: -1. Fibromuscular dysplasia -2. Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) -3. Spontaneous arterial dissection -4. Giant cell arteritis -5. Isolated angiitis of the central nervous system -6. Moyamoya disease -7. Collagen vascular disease (e.g. Ehlers-Danlos syndrome, Marfan syndrome) -8. Neurofibromatosis type 1 -9. Systemic lupus erythematosus -10. Polyarteritis nodosa -11. Segmental arterial mediolysis -12. Cocaine or other stimulant use" -PMID_33471980-case.txt leaving us with two possible diagnoses: myocarditis or a large myocardial infarction. When all the features of this patient’s presentation are considered, her primary diagnosis was most likely biventricular cardiomyopathy due to either myocarditis or pregnancy-associated myocardial infarction. Owing to the severity of the ventricular dysfunction, a myocardial infarction would have probably involved the left main coronary artery or multiple coronary arteries. To further refine the differential diagnosis, I would recommend coronary angiography to evaluate the coronary arteries and, if possible, native endomyocardial biopsy, recognizing that the patient is currently receiving anticoagulation for the ECMO circuit. "Most Likely Diagnosis: Peripartum cardiomyopathy complicated by ventricular tachycardia and cardiogenic shock, along with deep vein thrombosis. - -Differential Diagnoses, from most likely to least likely: -1. Peripartum cardiomyopathy -2. Myocardial infarction -3. Acute heart failure due to other causes, such as myocarditis -4. Pre-eclampsia or HELLP syndrome -5. Massive pulmonary embolism -6. Severe sepsis or septic shock -7. Drug-induced cardiac dysfunction -8. Thrombotic thrombocytopenic purpura or other thrombotic microangiopathies -9. Amniotic fluid embolus -10. Pulmonary hypertension due to other causes." -PMID_36069875-case.txt Neuro-Behçet’s disease. "Most Likely Diagnosis: Neuro-Behcet's disease - -Differential Diagnoses: - -1. Neuro-Behcet's disease -2. Meningitis (Bacterial, Fungal) -3. Herpes Simplex Virus-1 (HSV-1) or HSV-2 encephalitis -4. Neurological manifestations due to systemic lupus erythematosus (SLE) -5. NeuroSarcoidosis -6. Central nervous system (CNS) Vasculitis -7. Multiple sclerosis -8. Neurological manifestation of coronavirus disease 2019 -9. Tuberculosis meningitis -10. Neurological manifestations of acute HIV infection. -11. Neurosyphilis -12. Cerebral abscess -13. Lymphoma (particularly CNS lymphoma) -14. Neurological manifestations of autoimmune encephalitis. -15. Subdural empyema -16. Neurological manifestations of lymphocytic choriomeningitis -17. Neurological manifestations of Lyme disease." -PMID_33596360-case.txt Disseminated bacille Calmette–Guérin infection. "OPENAI API CALL FAILED" -PMID_34233100-case.txt In this patient with the triad of cerebellar ataxia, neuropathy, and bilateral vestibular dysfunction, the clinical syndrome of CANVAS is the most likely diagnosis. Given the patient’s family history of a shuffling gait and celiac disease, immune and genetic causes of this syndrome should be ruled out. "Most Likely Diagnosis: Sensory and autonomic neuropathy with cerebellar ataxia caused by Friedreich's Ataxia - -Differential Diagnoses in order of likelihood: - -1. Sensory and autonomic neuropathy with cerebellar ataxia caused by Friedreich's Ataxia -2. Autonomic and sensory neuropathy caused by Autosomal Dominant Sensory Ataxia (ADSA) -3. Cerebellar Ataxia, Neuropathy, Vestibular Areflexia syndrome (CANVAS) -4. Neurological manifestation of Systemic Lupus Erythematosus (SLE) -5. Neurological manifestation of Sjögren's syndrome. -6. Multiple System Atrophy (MSA) -7. Olivopontocerebellar atrophy (OPCA) -8. Cerebellar variant of Multiple System Atrophy (MSA-C) -9. Paraneoplastic cerebellar degeneration as a consequence of occult malignancy. -10. Widespread neoplasm metastasis including CNS. -11. Spinocerebellar ataxias (SCA, Despite negative genetic testing for common SCAs -SCA1, SCA2, SCA3, SCA6, and SCA8) -12. Peripheral Nerve Hyperexcitability (PNH) due to Voltage-gated Potassium Channel Complex Antibodies (VGKC) -13. Autoimmune or paraneoplastic cerebellar ataxia -14. Neurological manifestation of celiac disease (defined by the familial pattern and absence of celiac disease antibodies) -15. Drug-induced cerebellar degeneration (unsure if any medications taken by the patient may cause this syndrome) -16. Alcohol-related cerebellar degeneration." -PMID_35857663-case.txt a feature that is consistent with this patient’s test result. Furthermore, there is known cross-reactivity between urine tests for histoplasma and blastomyces antigens, which could account for this patient’s positive histoplasma antigen test. Coupled with her epidemiologic risk factors, including soil exposure in Vermont and Canada, I suspect that she has blastomycosis. To establish the diagnosis of blastomycosis, I would await maturation of the fungal cultures; if they are negative, I would pursue transbronchial biopsy of the cavitary lesions for fungal staining and culture. "Most Likely Diagnosis: Ectopic adrenocorticotropic hormone (ACTH) secretion by a metastatic pancreatic neuroendocrine tumor, with concurrent Histoplasmosis infection. - -Differential Diagnoses: - -1. Ectopic adrenocorticotropic hormone (ACTH) secretion by a metastatic pancreatic neuroendocrine tumor: Supported by elevated cortisol & ACTH levels, presence of pancreatic exophytic mass, multiple metastases, histopathological findings in pituitary biopsy inconsistent with corticotroph adenoma, and no history of tuberculosis skin test positivity, differential effects on psychological health with etomidate, lorazepam interventions, and subsequent positive effects after bilateral adrenalectomy and cortisol management. - -2. Cushing's disease secondary to a recurrent pituitary corticotroph adenoma: Despite failing two operations and a pathology report inconsistent with this diagnosis, the history of two pituitary surgeries, residual pituitary lesion and ongoing high cortisol & ACTH levels could suggest persistent pituitary origin. - -3. Adrenal Cushing's syndrome: Presence of adrenal gland thickening could suggest an adrenal source of excess cortisol, although the ACTH levels would not typically be high in this scenario. - -4. Adrenal Carcinoma: The adrenal thickening and elevated cortisol levels could also suggest this diagnosis, however, the ACTH levels are inappropriately high for this setting. - -5. Chronic histoplasmosis infection: Supported by the positive urine test for histoplasma antigen, imaging findings in the right upper lung lobe and presence of immunosuppressive states (Cushing's Syndrome), but negative BAL fluid culture. - -6. Secondary bacterial pneumonia: Demonstrated by growth of Staphylococcus aureus in BAL fluid and imaging findings, but other concurrent infections may be more likely. - -7. Tuberculosis infection: A less likely diagnosis but always a consideration in individuals with immune deficits, despite the negative history of skin testing and no growth of acid-fast bacilli colonies in cultures so far. - -8. Latent autoimmune diabetes in adults (LADA) or type 2 diabetes: Supported by the patient being on metformin. - -9. Central diabetes insipidus: Evidenced by the fact that the patient is being treated with desmopressin. - -10. Hypothyroidism: The patient is being treated with levothyroxine, suggesting this condition, but not related to the primary pathologies in this case. - -11. Asthma: It is in the medical history, but not relevant in this current clinical scenario. - -12. Portal-vein thrombosis with ascites: Part of patient's past medical history but unrelated to current clinical syndrome." -PMID_33913642-case.txt Dr. Dorit Koren’s Initial Diagnosis "Most Likely Diagnosis: Cervical neuroblastoma - -Differential Diagnoses, Ranked by Probability: -1. Cervical neuroblastoma: This tumor arises from the sympathetic chain and often presents as a neck mass in neonates. The presence of displacement of the trachea without compression, along with the markedly hypervascular ultrasound image supports this diagnosis. -2. Cervical teratoma: These are often large, vascular neck masses. The baby's increased alpha-fetoprotein levels may point to this diagnosis; however, these tumors are usually heterogeneous (containing various tissue types) and the mass in this case appears homogenous on ultrasound. -3. Cervical lymphangioma: These benign, lymphatic malformations can present as a neck mass in newborns. However, they are typically multicystic; this mass appears solid in imaging. -4. Other neck masses such as a branchial cleft cyst or thyroid goiter: While both of these can present as neck masses in newborns, neither is consistent with the imaging findings and other clinical characteristics of this case. -5. Less likely differential diagnoses in a newborn can include a thymic cyst, thyroid adenoma, or parathyroid adenoma, but these all seem less likely given the clinical and radiologic findings presented here. - -Diagnostic tests to be performed: From the case, it appears a diagnostic procedure is performed, likely a biopsy of the mass. The definitive diagnosis of these conditions is often made by histological examination of the mass tissue. Additional ancillary tests, such as immunohistochemistry or cytogenetic studies, can further support the diagnosis." -PMID_35544390-case.txt The biopsy specimens were generally small and were not targeted to the abnormalities observed on CT, because the biopsy was not performed with CT guidance. B-cell lymphoma remained at the top of the differential diagnosis, so the patient next underwent a CTguided transabdominal liver biopsy, which allowed the proceduralist to attempt to visualize the targeted area of interest. "Most likely diagnosis: Whipple's disease - -Differential diagnosis, ranked by probability: -1. Whipple's disease -2. Lymphangiectasia -3. Gastroparesis secondary to autonomic neuropathy -4. Carcinoid syndrome -5. Liver cirrhosis -6. Eosinophilic gastroenteritis -7. Tropical sprue -8. Systemic lupus erythematosus (SLE) -9. Capillary leak syndrome -10. Erdheim-Chester disease." -PMID_36070713-case.txt Thus, the negative test result does not dissuade me from making a diagnosis of candida meningitis. I suspect the diagnostic test was a CSF fungal culture. "Most Likely Diagnosis: -Neurocysticercosis - -Differential Diagnosis Ranked by Likelihood: -1. Neurocysticercosis -2. Tuberculoma -3. Lymphoma -4. Neurosarcoidosis -5. Brain abscess -6. Metastatic cancer -7. Bacterial Meningitis -8. Viral Meningitis -9. Cryptococcal Meningitis -10. Pseudotumor cerebri -11. Intracranial hemorrhage." -PMID_36383716-case.txt carina, and transbronchial needle aspiration was subsequently performed. Dr. Daniel Shepherd: During fine-needle aspiration of the subcarinal mass, a rapid on-site evaluation of the specimen was performed. Hematoxylin and eosin staining (Fig. 3A and 3B) showed clusters of large epithelioid cells with anisonucleosis, irregularly contoured nuclei, prominent nucleoli, and occasional binucleated forms. There was a moderate amount of thin, delicate eosinophilic cytoplasm with occasional intracytoplasmic mucin. These findings are consistent with poorly differentiated adenocarcinoma. No morphologic features of small-cell carcinoma were seen, and immunohistochemical staining for neuroendocrine markers and for programmed death ligand 1 (PD-L1) was negative. Dr. Dudzinski: Radiation and medical oncology management decisions were made. "My most likely diagnosis, based on the clinical history and diagnostic findings, is Non-Small Cell Lung Cancer (NSCLC), specifically poorly differentiated adenocarcinoma type. - -Here is my ranked differential diagnosis: - -1. Non-Small Cell Lung Cancer (NSCLC) - poorly differentiated adenocarcinoma -2. Squamous cell carcinoma of the lung -3. Small Cell Lung Cancer (SCLC) -4. Lymphoma -5. Metastatic extrathoracic cancer -6. Granulomatous thoracic infection -7. Fibrosing mediastinitis -8. Superior vena cava syndrome (as a secondary condition due to growth of lung tumor) -9. Paraneoplastic syndrome (the symptoms may indicate this, however, this is likely secondary to the cancer diagnosis) -Some of these possibilities may not be viewed as separate diagnoses, but rather extensions or different presentations of the primary condition (NSCLC). However, given the presented symptoms, pathology, and imaging, these are the potential conditions that could be considered. Further testing would help to rule out or confirm these differential diagnoses." -PMID_35830644-case.txt help to refine the differential diagnosis, the definitive test in this case would be a kidney biopsy to establish the cause of the kidney disease. "Most Likely Diagnosis: -ANCA-associated vasculitis (granulomatosis with polyangiitis or microscopic polyangiitis) - -Differential Diagnoses (from most likely to least): -1. ANCA-associated vasculitis (granulomatosis with polyangiitis or microscopic polyangiitis) -2. Goodpasture syndrome -3. Systemic Lupus Erythematosus -4. Infectious pneumonia (bacterial, viral such as COVID-19, or fungal) -5. Acute tubular necrosis secondary to systemic infection -6. Diffuse alveolar hemorrhage, secondary to another systemic condition -7. Wegener’s Granulomatosis (sub-type of ANCA Vasculitis) -8. Foreign body aspiration pneumonia -9. Post-infectious Glomerulonephritis -10. Immune complex kidney disease -11. Membranoproliferative glomerulonephritis -12. Organizing pneumonia." -PMID_35320647-case.txt ranges from 5 to 21 days. Leukopenia is present in the majority of patients; the white-cell count in this patient was near the low end of the normal range. No findings on chest CT are specific for anaplasmosis. The CT findings observed in this case (interlobular septal thickening, groundglass opacities, and pleural effusions) are nonspecific and can be seen with a wide array of atypical infections, as well as noninfectious causes. The main contribution of the imaging findings in this case was to assist in ruling out other possible explanations of the patient’s symptoms, such as typical bacterial pneumonia. Human ehrlichiosis may mimic anaplasmosis, but one third of patients with ehrlichiosis have a maculopapular or petechial rash, which was not present in this patient. Also, ehrlichiosis is less likely to be associated with thrombocytopenia than is human granulocytic anaplasmosis. On the basis of the constellation of these findings, I overcame my bias toward Covid-19 and considered tickborne infection, particularly anaplasmosis, to be the most likely diagnosis in this patient. To establish this diagnosis, we performed additional testing, including blood testing for Lyme disease antibodies, an examination of thick and thin blood smears for babesia, and nucleic acid testing for A. phagocytophilum DNA. "Most Likely Diagnosis: Acute viral syndrome due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), or COVID-19. - -Robust Differential Diagnosis: - -1. COVID-19: Despite the negative nasopharyngeal test result, the patient's symptoms align with SARS-CoV-2. False negatives occur in testing. -2. Influenza: Symptoms of flu can be similar to COVID-19, and this cannot be completely ruled out despite negative testing for influenza viruses A and B. -3. Community-Acquired Pneumonia: Negative tests for common bacterial and viral causes do not rule out all potential pathogens. -4. Non-SARS-CoV-2 Coronavirus: Other coronaviruses can cause similar symptoms to COVID-19. -5. Atypical Bacterial Infection: Though less likely, given the negative tests for common atypical bacteria, it is not completely ruled out. -6. Tuberculosis: The chest imaging findings could be suggestive of TB, especially given the patient's urban dwelling status. -7. Legionnaire's Disease: The patient has been mostly at home but the potential for exposure through a contaminated water supply cannot be ruled out. -8. Q Fever: This can present with similar findings, though there is no mention of known exposure to farm animals. -9. Lyme Disease: Lyme disease may sometimes present with fever, myalgia and headache, and contact with wooded areas is a risk factor. -10. Brucellosis: Although the patient has no significant travel history or known exposure to unpasteurized dairy, cannot be completely ruled out. -11. Autoimmune/Connective Tissue Disease: In the unlikely event of this being an acute presentation of such a disease. - -The final diagnosis is likely to depend upon the results of the diagnostic test performed on the eighth hospital day." -PMID_36516093-case.txt Because of the need to rule out adrenocortical carcinoma, laparoscopic right adrenalectomy was performed. "Most Likely Diagnosis: Cushing’s syndrome due to an adrenal adenoma - -Differential Diagnoses (from most likely to least likely): -1. Cushing's syndrome due to an adrenal adenoma -2. Adrenocortical carcinoma -3. Ectopic adrenocorticotropic hormone (ACTH) syndrome -4. Hypothyroidism-associated fatigue and weight gain -5. Pheochromocytoma -6. Non-functional adrenal tumor -7. Polycystic ovary syndrome-induced weight gain and fatigue -8. Iatrogenic Cushing's syndrome from corticosteroid use -9. Cushing's syndrome due to pituitary adenoma (Cushing's disease) -10. Adrenal hyperplasia -11. Adrenal metastases from an unknown primary -12. Paraneoplastic syndrome from an undiagnosed malignancy -13. Familial syndromes that include adrenal tumors, such as Multiple Endocrine Neoplasia Type 1 -14. Functional adrenocortical oncocytoma." -PMID_34818483-case.txt Cutaneous bacterial infection. "Most Likely Diagnosis: -Septicemia due to Gram-negative bacteria, likely Pseudomonas aeruginosa or E. coli, contracted from handling the deer hide in the process of taxidermy. - -Differential Diagnosis (from most to least likely): -1. Infectious cellulitis - likely bacterial, related to exposure from deer hide or ticks. -2. Necrotizing fasciitis - possibly contracted from deer hide or tick exposure. -3. Lyme disease - caused by tick bites, possible tick exposure from deer hide. -4. Pasteurella infection - possible exposure from the animal hide. -5. Tularemia - possible exposure from deer hide or ticks. -6. Pyogenic joint infection or septic arthritis - possible pathogen exposure from deer hide. -7. Tick-born illnesses (other than Lyme disease) - ehrlichiosis, babesiosis, anaplasmosis due to tick removal from deer hide. -8. Mycobacterium marinum infection - this is a lower probability, but may be contracted from handling raw hides or skins, particularly if there were any direct traumatic exposure. -9. Anthrax (cutaneous) - possible exposure from handling of deer hide. -10. Rat-bite fever - exposure possible from handling of raw hide. -11. Rabies - very low probability, but possible exposure through handling of a raw hide from a potentially infected animal." -PMID_34289280-case.txt No single clue from the history, imaging studies, or laboratory test results in this case is specific for a diagnosis, and I suspect that a brain and meningeal biopsy was ultimately required to establish a pathological diagnosis and direct treatment. Reasonable diagnostic possibilities include varicella–zoster virus meningoencephalitis, neurosarcoidosis, primary CNS vasculitis, and CAA-related inflammation. Because of the presence of multiple hemorrhagic lesions in the brain on MRI, I think that CAA-related inflammation is the most likely diagnosis in this case. "Most Likely Diagnosis: Autoimmune encephalitis (AE) - -Differential Diagnosis, in order of likelihood: - -1. Limbic encephalitis (LE) -2. Multiple Sclerosis (MS) -3. Central Nervous System vasculitis (CNS) -4. Creutzfeldt-Jakob Disease (CJD) -5. Neurosarcoidosis -6. Lymphomatous meningitis -7. Central Nervous System Lymphoma (CNSL) -8. Neurosyphilis -9. Subacute Sclerosing Panencephalitis (SSPE) -10. Bacterial meningitis -11. Viral encephalitis -12. Prion disease -13. Alzheimer’s Disease (AD)." -PMID_35353965-case.txt Hypertrophic cardiomyopathy most likely due to Fabry’s disease. "Most Likely Diagnosis: Systemic amyloidosis, most likely senile cardiac amyloidosis (transthyretin-type) - -Differential Diagnosis (from most likely to least likely): - -1. Systemic amyloidosis, specifically senile systemic amyloidosis (transthyretin-type) -2. Hypertrophic cardiomyopathy -3. Idiopathic restrictive cardiomyopathy -4. Fabry disease -5. Anderson-Fabry disease -6. Endomyocardial fibrosis -7. Sarcoidosis -8. Lyme disease-induced cardiomyopathy -9. Loeffler endomyocarditis -10. Mitochondrial disease-induced cardiomyopathy -11. Cardiac hemochromatosis (iron overload cardiomyopathy) -12. Cardiac sarcoidosis -13. Danon disease -14. Rare infiltrative storage diseases like Gaucher’s disease -15. Carcinoid heart disease. -16. Metastatic neoplasm causing restrictive cardiomyopathy." -PMID_34042393-case.txt tion of the aorta were ultimately required. The endograft was placed in a percutaneous manner through the common femoral arteries on the day that the patient was transferred to this hospital. The graft lined the aorta from the level below the renal arteries to the level of the bilateral common iliac arteries to prevent acute aortic rupture and hemorrhagic death from occurring while the final diagnosis was being determined. "Most likely diagnosis: Infective Endocarditis - -Differential Diagnosis (ranked from most likely to least likely): - -1. Infective Endocarditis -2. Vasculitides, possibly Giant Cell Arteritis (Temporal Arteritis) -3. Polyarteritis Nodosa -4. Rheumatic Fever -5. Disseminated Intravascular Coagulation -6. Sepsis/septic shock -7. Abdominal aortic aneurysm -8. Acute mesenteric ischemia -9. Granulomatosis with polyangiitis (previously known as Wegener’s granulomatosis) -10. Tuberculosis -11. Bacterial Meningitis -12. Reiter's Syndrome -13. Heroin or substance use related infection or vasculitis -14. Chiari I-related complications" -PMID_34133863-case.txt However, in clinical medicine, patient presentations often do not fit these maxims, and this is one clinical situation in which a life-threatening diagnosis — acute pulmonary embolism — must be ruled out. Therefore, in addition to testing the patient’s nasopharyngeal specimen for SARS-CoV-2 RNA to establish the diagnosis of Covid-19, I would recommend obtaining a computed tomographic (CT) pulmonary angiogram to identify pulmonary embolism. "Most likely diagnosis: COVID-19 pneumonia complicated with Acute Respiratory Distress Syndrome (ARDS). - -Differential Diagnosis, ranked by probability: -1. COVID-19 pneumonia with ARDS -2. Pulmonary embolism secondary to COVID-19 -3. Bacterial pneumonia superinfection with underlying COVID-19 -4. Heart failure secondary to myopericarditis due to COVID-19 -5. Pulmonary fibrosis with acute exacerbation -6. Pneumothorax or hemothorax, possibly from a fall as reported by patient’s son -7. Pleuritis or Pleural effusion secondary to pneumonia or other infection -8. Pulmonary tuberculosis reactivation aggravated by COVID-19." -PMID_35613025-case.txt This patient meets all consensus diagnostic criteria for iMCD except for the histologic features in lymph node tissue, so a second review of the specimen is warranted. "Most Likely Diagnosis: Disseminated histoplasmosis. - -Differential Diagnosis, from most likely to least likely: -1. Disseminated histoplasmosis. -2. Disseminated tuberculosis. -3. Non-Hodgkin's lymphoma. -4. Metastatic carcinoma. -5. Sarcoidosis. -6. Systemic lupus erythematosus. -7. Anaplasmosis. -8. Brucellosis. -9. Parvovirus B19 infection. -10. Castleman's disease." From a90df854d563ff869435fa51fa2eedadfdc9c8d2 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Thu, 18 Jul 2024 18:05:57 -0400 Subject: [PATCH 04/40] Remove phenopacket_based_queries_results.tsv --- phenopacket_based_queries_results.tsv | 1466 ------------------------- 1 file changed, 1466 deletions(-) delete mode 100644 phenopacket_based_queries_results.tsv diff --git a/phenopacket_based_queries_results.tsv b/phenopacket_based_queries_results.tsv deleted file mode 100644 index 2aa36599f..000000000 --- a/phenopacket_based_queries_results.tsv +++ /dev/null @@ -1,1466 +0,0 @@ -input file name correct diagnosis gpt diagnosis -PMID_33704941-phenopacket-based_query.txt and neurologic findings, we suspected that the trigger was meningococcal disease. "Based on the presented signs and symptoms, the most likely diagnosis: - -Acute Respiratory Distress Syndrome (ARDS) secondary to Pneumonia (possibly bacterial in nature given the presence of chills and potential meningitis). - -Differential Diagnosis, ranked by probability: -1. Acute Respiratory Distress Syndrome (ARDS) secondary to Pneumonia. -2. Chronic obstructive pulmonary disease (COPD) exacerbated by Pneumonia. -3. Congestive Heart Failure (CHF) with secondary Pulmonary Edema. -4. Severe Sepsis or Septic Shock, possibly due to Meningococcal Meningitis. -5. Viral illness such as severe Influenza or COVID-19. -6. Pulmonary Embolism (PE) with infarction. -7. Aspiration pneumonia due to alcoholism. -8. Myxedema coma due to severe Hypothyroidism. -9. Guillain-Barré Syndrome. -10. Systemic Lupus Erythematosus (SLE) with Lupus Nephritis. -11. Neuroleptic Malignant Syndrome (possible drug-induced). -12. Acute exposure to toxic substances or overdose. - -The expected tests to confirm a diagnosis in this case administration would likely consist of a full blood profile (including a blood culture), chest x-ray, echocardiogram, pulmonary function test, thyroid function tests, and a spinal tap for potential bacterial meningitis. A consultation with a psychiatrist might also be beneficial given the presence of anxiety and depression." -PMID_35767442-phenopacket-based_query.txt pected and, in the context of the PET-CT findings, was suggestive of PTLD related to plasmacell myeloma or non-Hodgkin’s lymphoma with associated monoclonal protein. Given the possible diagnosis of PTLD, we elected to proceed with biopsy of a lymph node in the inguinal region, which was the most easily accessible area with lymphadenopathy. "Most likely diagnosis: -Relapse/Progression of Acute Lymphoblastic Leukemia (ALL). - -Differential Diagnostics: -1. Relapse/Progression of Acute Lymphoblastic Leukemia -2. Infection, particularly pulmonary infection, secondary to immunosuppression in ALL -3. Anemia due to Bone Marrow Suppression in ALL -4. Chronic Heart Failure or Cardiac Dysfunction secondary to therapy (Chemotherapy-related cardiotoxicity) -5. Pulmonary Embolism -6. Tuberculosis -7. Pneumonia -8. Chronic Obstructive Pulmonary Disease (COPD) -9. Acute Respiratory Distress Syndrome (ARDS) -10. Pulmonary Hypertension -11. Anxiety disorder causing dyspnea -12. Asthma." -PMID_34551232-phenopacket-based_query.txt performed to obtain a more sensitive view of the joints and to rule out occult osteomyelitis and tumor. The presence of widespread lymphadenopathy on MRI would further support the diagnosis of systemic juvenile idiopathic arthritis. If arthritis were absent but more accessible lymph nodes were identified, diagnostic biopsy would have been considered. "Most Likely Diagnosis: -Myasthenia Gravis - -Differential Diagnoses ordered by their likelihood: -1. Myasthenia Gravis -2. Congenital Myasthenic Syndrome -3. Lambert-Eaton Syndrome -4. Hyper IgM Syndrome -5. Congenital Muscular Dystrophy -6. Pancreatic Cancer -7. Hypothyroidism -8. Autism Spectrum Disorder -9. Down Syndrome -10. Neonatal Myasthenia Gravis -11. Neuroblastoma -12. Sjogren's Syndrome -13. Miller Fisher Syndrome -14. Kearns-Sayre Syndrome -15. Chronic Fatigue Syndrome -16. Chronic Granulomatous Disease -17. Breast Carcinoma (very unlikely, more of a coincidental finding than causative) -18. Cystic Fibrosis -19. Duchenne Muscular Dystrophy -20. Rare syndromic/non-syndromic genetic disorders -21. Acute disseminated encephalomyelitis (ADEM) -22. Guillain-Barré Syndrome -23. Rhabdomyolysis." -PMID_35544390-phenopacket-based_query.txt The biopsy specimens were generally small and were not targeted to the abnormalities observed on CT, because the biopsy was not performed with CT guidance. B-cell lymphoma remained at the top of the differential diagnosis, so the patient next underwent a CTguided transabdominal liver biopsy, which allowed the proceduralist to attempt to visualize the targeted area of interest. "Based on the provided symptoms, I will make the following preliminary diagnosis. - -Most Likely Diagnosis: Liver Cirrhosis - -Differential Diagnosis: - -1. Liver Cirrhosis -2. Heart Failure -3. Nephrotic Syndrome -4. Malnutrition -5. Chronic Pancreatitis -6. Budd-Chiari Syndrome -7. Peritoneal Carcinomatosis -8. Constrictive Pericarditis -9. Portal Vein Thrombosis -10. Tuberculosis Peritonitis" -PMID_35139277-phenopacket-based_query.txt Diagnostic Testing "Most likely diagnosis: -Cogan’s Syndrome - - -Differential Diagnoses, From Most Likely to Least Likely: - -1. Cogan’s Syndrome -2. Meniere's Disease -3. Migraine related vertigo -4. Non-specific autoimmune disease (like rheumatoid arthritis) -5. Temporal Arteritis (Giant cell arteritis) -6. Neurosyphilis -7. Vasculitis (like Wegener’s granulomatosis) -8. Acute viral labyrinthitis -9. Multisystem disease like sarcoidosis -10. Chronic Fatigue Syndrome -11. Lyme Disease -12. Multiple Sclerosis -13. Inner ear pathology like acoustic neuroma or otitis media -14. Non-specific upper respiratory tract disorder." -PMID_36577103-phenopacket-based_query.txt In this patient with episodic exertional chest discomfort, a flushing syndrome 15 years earlier, and an intracardiac mass, we hypothesized that intratumoral metabolism may have been altered over time and become restricted to dopamine production. With the assistance of a multidisciplinary team of specialists — including specialists in cardiology, interventional cardiology, oncology, radiation oncology, endocrinology, cardiac anesthesia, and cardiac surgery — we developed a plan for perioperative and long-term management. "Most Likely Diagnosis: -Mastocytosis, specifically systemic mastocytosis given the wide array of symptoms affecting multiple organ systems. - -Differential Diagnoses List: -1. Mastocytosis (Systemic) -2. Carcinoid syndrome -3. Paraneoplastic syndromes due to colon cancer -4. Allergic reaction/Anaphylaxis -5. Multiple Endocrine Neoplasia type IIb -6. Pheochromocytoma -7. Vasculitis, specifically Churg-Strauss Syndrome -8. Adrenal insufficiency -9. Congestive heart failure secondary to ventricular arrhythmias -10. Hyperthyroidism -11. Acute stress reaction or panic disorder -12. Vasovagal syncope -13. Inflammatory bowel disease -14. Neuroendocrine tumor other than carcinoid -15. Chronic obstructive pulmonary disease (COPD) exacerbation complicated by heart failure -16. Heart block -17. Idiopathic urticaria and angioedema" -PMID_35045230-phenopacket-based_query.txt VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome. "Based on the case description, my most likely diagnosis is: - -Relapsing Polychondritis. - -Here is my differential diagnosis, listed in order from most to least likely: - -1. Relapsing Polychondritis -2. Systemic Lupus Erythematosus (SLE) -3. Granulomatosis with Polyangiitis (Wegener's) -4. Microscopic Polyangiitis -5. Sarcoidosis -6. Vasculitis associated with Rheumatoid Arthritis -7. Behcet's Disease -8. Systemic Sclerosis (Scleroderma) -9. Giant Cell Arteritis -10. Polyarteritis Nodosa." -PMID_35294816-phenopacket-based_query.txt of C4, C1 inhibitor, and C1q, as well as a repeat assessment of C1 inhibitor function, to further investigate her previous diagnosis of acquired C1 inhibitor deficiency and the possibility of a diagnosis of hereditary angioedema with C1 inhibitor deficiency. "Most likely diagnosis: Carcinoid syndrome - -Differential diagnosis, ranked by probability: -1. Carcinoid syndrome -2. Systemic mastocytosis -3. Zollinger-Ellison syndrome -4. Pheochromocytoma -5. Atypical pneumonia -6. Sarcoidosis -7. Systemic lupus erythematosus -8. Multiple endocrine neoplasia type 1 (MEN1) -9. Vasculitis -10. Cushing's syndrome -11. Autoimmune polyglandular syndrome type I -12. Celiac disease -13. Addison's disease -14. Chronic pancreatitis -15. Tuberculosis -16. Hyperthyroidism -17. Chronic heart failure." -PMID_35857663-phenopacket-based_query.txt a feature that is consistent with this patient’s test result. Furthermore, there is known cross-reactivity between urine tests for histoplasma and blastomyces antigens, which could account for this patient’s positive histoplasma antigen test. Coupled with her epidemiologic risk factors, including soil exposure in Vermont and Canada, I suspect that she has blastomycosis. To establish the diagnosis of blastomycosis, I would await maturation of the fungal cultures; if they are negative, I would pursue transbronchial biopsy of the cavitary lesions for fungal staining and culture. "Based on the presented symptoms, my most likely diagnosis is Cushing’s disease. - -Differential diagnoses, arranged in the order of likelihood: -1. Cushing’s disease -2. Exogenous corticosteroid use -3. Ectopic ACTH syndrome -4. Addison's disease -5. Adrenocortical carcinoma -6. Polycystic ovary syndrome (PCOS) -7. Insulinoma -8. Metabolic syndrome -9. Chronic pancreatitis -10. Primary biliary cirrhosis." -PMID_34525289-phenopacket-based_query.txt and have relevance to patients presenting for medical care in the context of the current pandemic. The underlying principles are that persons with psychiatric disorders need to be identified and connected with appropriate psychiatric care and that the distress of other members of affected populations is best addressed through psychosocial interventions, such as psychological first aid, without labeling the normative responses to disaster trauma as abnormal. This patient will benefit from observation for the development of a recurrent depressive or anxiety disorder, as well as attention to address her understandable emotional distress. A mental health professional can assess any psychiatric illness that may develop and can assist in the psychosocial aspects of her recovery from her illness through psychotherapeutic interventions including psychosocial support, education, reassurance, and assistance with resumption of her previous level of functioning. In my opinion, this patient is having understandable psychosocial distress in the context of a serious medical illness during the Covid-19 pandemic. The key to understanding this case is to acknowledge that this patient’s distress is a normative response and does not meet criteria for a psychiatric diagnosis. "Most Likely Diagnosis: COVID-19 (SARS-CoV-2 infection) - -Differential Diagnoses (Ranked): - -1. COVID-19 (SARS-CoV-2 infection) -2. Influenza (Flu) -3. Pneumonia (non-COVID-19) -4. SARS/MERS -5. Anxiety Disorder with somatic symptoms -6. Major Depressive Disorder with somatic symptoms -7. Chronic Fatigue Syndrome -8. Lyme Disease -9. HIV Initial Infection Stage -10. Tuberculosis -11. Mononucleosis (Epstein-Barr virus) -12. Community-acquired pneumonia -13. Generalized Anxiety Disorder -14. Panic Disorder -15. Migraine (Chronic) -16. Systemic Lupus Erythematosus -17. Chronic Obstructive Pulmonary Disease (COPD) -18. Gastroenteritis -19. Postural Orthostatic Tachycardia syndrome -20. Middle East Respiratory Syndrome (MERS-CoV) -21. Asthma with a respiratory tract infection -22. Viral syndrome -23. Bronchitis -24. Gastroparesis -25. Guillain-Barre Syndrome -26. Multiple Sclerosis -27. Meniere's Disease -28. Autonomic Dysfunction -29. Grave's Disease -30. Myasthenia Gravis -31. Addison’s Disease." -PMID_34042393-phenopacket-based_query.txt tion of the aorta were ultimately required. The endograft was placed in a percutaneous manner through the common femoral arteries on the day that the patient was transferred to this hospital. The graft lined the aorta from the level below the renal arteries to the level of the bilateral common iliac arteries to prevent acute aortic rupture and hemorrhagic death from occurring while the final diagnosis was being determined. "The most likely diagnosis: - -1. Infectious aortitis - -Robust differential diagnosis: - -1. Infectious aortitis, possibly secondary to Salmonella or Staphylococcus aureus -2. Abdominal aortic aneurysm rupture complicated by systemic infection -3. Vasculitis, such as Giant cell arteritis or Takayasu's arteritis -4. Intra-abdominal abscess formation, possibly secondary to appendicitis or diverticulitis -5. Pancreatitis with secondary infection -6. Sepsis secondary to urinary tract infection -7. Bacterial endocarditis with aneurysm formation -8. Marfan syndrome leading to aortic aneurysm and systemic symptoms due to associated conditions -9. Non-infectious aortic inflammation, such as non-infectious aortitis -10. Systemic lupus erythematosus which can involve both visceral and vascular inflammation -11. Aortic dissection with secondary infection. -12. Congenital connective tissue disorders like Ehlers-Danlos syndrome leading to aortic aneurysms. -13. Syphilitic aortitis (although much less likely given demographic). -14. Abdominal malignancy with secondary infection causing fever, nausea, vomiting, and chills." -PMID_36103417-phenopacket-based_query.txt GPA is initially responsive to glucocorticoids, but remission requires treatment with either the cytotoxic drug cyclophosphamide or the B-cell– depleting antibody rituximab. Rituximab takes time to work and would not yet have been effective within the 2 weeks after treatment, when this patient’s radiologic findings had progressed and clinical deterioration had occurred. "Most likely diagnosis: -Giant Cell Arteritis - -Differential diagnosis list: -1. Giant Cell Arteritis -2. Temporal Arteritis -3. Polymyalgia Rheumatica -4. Horton Disease -5. Takayasu Arteritis -6. Rheumatoid Arthritis -7. Systemic Lupus Erythematosus -8. Fibromyalgia -9. Systemic Vasculitis -10. Behcet's disease -11. Sarcoidosis -12. Lyme Disease -13. HIV/AIDS -14. Tuberculosis -15. Adult Onset Still's disease -16. Lymphoma -17. Multiple Myeloma -18. Leukemia." -PMID_35675180-phenopacket-based_query.txt mixed connective-tissue disease. I would recommend further evaluation, including testing for anti–U1-ribonucleoprotein (RNP) antibodies and antinuclear antibodies (ANA), cardiac magnetic resonance imaging (MRI), and renovascular imaging. "My most likely diagnosis: Acute myocarditis secondary to a possible infection - -Differential diagnoses, ranked by probability: - -1. Acute myocarditis: The symptoms like fever, chest pain, abnormal EKG, myalgia, and syncope could point towards an inflammation of heart muscles, possibly due to a viral infection (gastroenteritis causing diarrhea, vomiting, poor appetite, and nausea can be a trigger). -2. Infectious mononucleosis: Could present with fever, chest pain, syncope, myalgia, and gastrointestinal symptoms like diarrhea, vomiting, nausea, and poor appetite. -3. Gastroenteritis: Would primarily explain the gastrointestinal symptoms (diarrhea, vomiting, nausea, poor appetite), as well as a general malaise like fever, myalgia. -4. Kawasaki disease: Common in children and teenagers. It can present with fever, diarrhea, vomiting, myalgia, and chest pain due to myocarditis and associated EKG changes. -5. Acute pericarditis: Fever, chest pain, and EKG changes could be due to inflammation of the pericardium around the heart. -6. Neoplastic conditions: The nevus could be a sign of a paraneoplastic syndrome, causing a variety of the listed symptoms, though this is less likely without more specific signs of malignancy. -7. Eosinophilic gastroenteritis: Would primarily account for gastrointestinal symptoms but eosinophilia can cause myocardial involvement as well. Quite rare though. -8. Addison’s disease: It can cause nausea, vomiting, poor appetite, myalgia, syncope, and hyperpigmentation (seen as nevus). Very rare with no obvious adrenal insufficiency symptoms, hence it's lower in my list. -9. Lyme disease: Transmission is rare in some areas, but would account for many of the nonspecific symptoms, including possible cardiac involvement (Lyme carditis). -10. Systemic lupus erythematosus: This autoimmune disease can cause a wide range of symptoms, including gastrointestinal and cardiac symptoms. - -We would need additional information and test results for a more accurate diagnosis, but these are the differentials based on the given symptoms." -PMID_34437787-phenopacket-based_query.txt splice acceptor variant was present at both the time of initial diagnosis and the time of relapse; this pattern is consistent with that observed in these similar cases. "Given the provided information, here are the most likely diagnosis and the differential diagnoses: - -Most Likely Diagnosis: -1. Chemotherapy-induced nausea, vomiting, and abdominal pain due to Acute Myeloid Leukemia (AML) treatment. - -Robust Differential Diagnoses: -1. Cholecystitis - Symptoms may be exacerbated due to potential hepatotoxic effects of AML or chemotherapy treatment. -2. Medication-induced nausea, vomiting and pain - Possible secondary effects of medications taken for AML. -3. Infection/sepsis - Patients with AML have compromised immune systems, which makes them vulnerable to a variety of infections. -4. Gastroenteritis - May present similarly and nausea/vomiting/pain could be caused by viral or bacterial infection. -5. Pancreatitis - A possible complication from the chemotherapy treatment. -6. Bowel obstruction - Could be related to drugs used in treatment regime or due to concomitant conditions. -7. Peptic ulcer disease - Stress and certain medications for chemotherapy can increase the risk." -PMID_36170504-phenopacket-based_query.txt Alternatively, if surgical resection of the mass is planned, pathological examination of the resection specimen can include an evaluation for islet cells. On the basis of the patient’s presentation with persistent hypoglycemia in the context of a probable sacrococcygeal teratoma, I suspect that the Sotos syndrome is the most likely diagnosis. To establish this diagnosis, targeted sequencing should be performed to identify variants in NSD1 . Alternatively, whole-exome sequencing could be performed in the infant, as well as in the parents if possible (trio approach), to identify pathogenic variants associated with genetic disorders that could be consistent with the patient’s clinical presentation, including the Sotos syndrome. "My likely diagnosis for this case is Congenital Disorders of Glycosylation (CDG). - -Here is my differential diagnosis ranked from most likely to least likely: - -1. Congenital Disorders of Glycosylation (CDG) -2. Multiple endocrine neoplasia type 1 (MEN1) -3. Septo-optic dysplasia (De Morsier’s Syndrome) -4. Niemann-Pick disease type C -5. Acrodermatitis enteropathica -6. Inborn errors of metabolism, such as Fructose intolerance -7. Wilson's Disease -8. Hypopituitarism -9. Progressive familial intrahepatic cholestasis type II -10. Shwachman-Diamond syndrome." -PMID_35353965-phenopacket-based_query.txt Hypertrophic cardiomyopathy most likely due to Fabry’s disease. "Based on the given case, here is my analysis: - -Most likely diagnosis: Metastatic Lung Cancer with secondary Cardiac Involvement (likely in the form of Atrial Fibrillation and Right Bundle Branch Block, possibly Hypertrophic Cardiomyopathy) and Chronic Thyroiditis. - -Differential Diagnosis, ranked by likelihood: -1. Metastatic Lung Cancer with secondary Cardiac Involvement and Chronic Thyroiditis -2. Chronic Obstructive Pulmonary Disease (COPD) with concomitant Primary Cardiomyopathy and Thyroiditis -3. Advanced Hypertrophic Cardiomyopathy with secondary Pulmonary Edema and Chronic Kidney Disease -4. Congestive Heart Failure with secondary Pulmonary Edema and Chronic Kidney Disease -5. Chronic Kidney Disease leading to Edema, Hypertension and Cardiac complications -6. Autoimmune Thyroid Disease with concomitant Lung Neoplasm and Cardiac complications -7. Polypharmacy side effects in an elderly patient leading to a wide array of symptoms -8. Metabolic Syndrome with subsequent Cardiovascular Disease, Chronic Kidney Disease, and Lung Cancer -9. Multiple System Atrophy with secondary Cardiac and Renal complications -10. Undifferentiated Connective Tissue disease resulting in multi-organ involvement." -PMID_34788511-phenopacket-based_query.txt was direct fluorescent antibody staining of an induced-sputum specimen to test for P. jirovecii . "Based on the provided information, my most likely diagnosis is: - -1. Autoimmune Hepatitis - -My differential diagnosis, ranked from most likely to least likely, includes: - -1. Autoimmune Hepatitis -2. Sarcoidosis -3. Primary Biliary Cirrhosis -4. Lupus (Systemic Lupus Erythematosus) -5. HIV infection/Acquired Immunodeficiency Syndrome (AIDS) -6. Chronic Granulomatous Disease -7. Common Variable Immunodeficiency -8. Hepatitis B/C -9. Non-Hodgkin's Lymphoma -10. Chronic Lymphocytic Leukemia." -PMID_33761211-phenopacket-based_query.txt -adrenergic receptors decrease insulin release and can cause hyperglycemia. Taken together, all the features suggest that the most likely diagnosis in this patient is pheochromocytoma. The first step in establishing this diagnosis is to perform abdominal imaging to look for an adrenal tumor consistent with pheochromocytoma. "Most Likely Diagnosis: Pheochromocytoma (adrenal gland tumor) - -Differential Diagnosis, from most likely to least likely: - -1. Pheochromocytoma (adrenal gland tumor) -2. Renal artery stenosis leading to hypertension -3. Cluster headache syndrome -4. Acute glaucoma -5. Eclampsia -6. Hyperthyroidism including Grave's Disease -7. Cushing's syndrome -8. Adrenal cortex cancer -9. Congenital adrenal hyperplasia -10. Acute alcohol withdrawal -11. Quadriplegic upper extremity pains secondary to spasticity -12. Hypokalemic periodic paralysis -13. Panic disorder -14. Carcinoid syndrome -15. Renal parenchymal disease -16. Pheochromocytoma secondary to Von Hippel-Lindau disease -17. Malignant hypertension -18. Polycystic ovary syndrome -19. Essential hypertension -20. Neuroblastoma, particularly paraneoplastic syndrome." -PMID_36477035-phenopacket-based_query.txt In this patient who had no risk factors for tuberculosis, the clinical syndrome of a progressive, fulminant illness with fever, innumerable pulmonary nodules, splenomegaly, and hypercalcemia occurring 7 months after kidney transplantation is most likely due to donor-derived infection with M. tuberculosis . Some patients may have risk factors for tuberculosis that are not identified initially, and once such risk factors are identified, a thorough requestioning of the patient is needed. To establish a diagnosis of tuberculosis, I would obtain pulmonary specimens for an acid-fast bacilli smear, nucleic acid amplification testing, and culture. I would begin the investigation by obtaining an induced sputum sample but would rapidly pursue bronchoscopy and biopsy of a pulmonary nodule if acid-fast staining and nucleic acid amplification testing are negative. I would evaluate concurrently for several of the diagnoses discussed previously, given the critical nature of this patient’s presentation and the possibility that an immunocompromised host may have multiple coexisting diseases at the time of presentation. "Most Likely Diagnosis: -Light Chain Deposition Disease (LCDD) - -Differential Diagnosis from most to least likely: -1. Light Chain Deposition Disease (LCDD) -2. Multiple myeloma -3. Primary Hyperparathyroidism -4. Renal Amyloidosis -5. Wilson's Disease -6. Lead Poisoning -7. Chronic Kidney Disease -8. Acute interstitial nephritis -9. Adult-onset Still's disease -10. Lupus nephritis -11. Sarcoidosis -12. Hepatitis B and C -13. Jarcho-Levin syndrome (spondylothoracic or spondylocostal dysostosis) -14. Alport syndrome -15. Hemochromatosis -16. Wegener's Granulomatosis -17. Systemic sclerosis -18. Chronic Pancreatitis -19. Lung Cancer -20. Addison's disease." -PMID_34289280-phenopacket-based_query.txt No single clue from the history, imaging studies, or laboratory test results in this case is specific for a diagnosis, and I suspect that a brain and meningeal biopsy was ultimately required to establish a pathological diagnosis and direct treatment. Reasonable diagnostic possibilities include varicella–zoster virus meningoencephalitis, neurosarcoidosis, primary CNS vasculitis, and CAA-related inflammation. Because of the presence of multiple hemorrhagic lesions in the brain on MRI, I think that CAA-related inflammation is the most likely diagnosis in this case. "As Dr. GPT-4, here is my evaluation: - -Most likely diagnosis: -Multiple Sclerosis - -Differential diagnosis (ranked from most likely to least likely): -1. Multiple Sclerosis -2. HIV associated neurocognitive disorder -3. Central nervous system lymphoma -4. Systemic Lupus Erythematosus (SLE) with Neuropsychiatric manifestations -5. Neuro-Behcet's disease -6. Neurosarcoidosis -7. Progressive Multifocal Leukoencephalopathy (PML) -8. CNS Vasculitis -9. Glioma -10. Neurosyphilis -11. Lyme Neuroborreliosis -12. Neuro-Whipple's disease " -PMID_35320647-phenopacket-based_query.txt ranges from 5 to 21 days. Leukopenia is present in the majority of patients; the white-cell count in this patient was near the low end of the normal range. No findings on chest CT are specific for anaplasmosis. The CT findings observed in this case (interlobular septal thickening, groundglass opacities, and pleural effusions) are nonspecific and can be seen with a wide array of atypical infections, as well as noninfectious causes. The main contribution of the imaging findings in this case was to assist in ruling out other possible explanations of the patient’s symptoms, such as typical bacterial pneumonia. Human ehrlichiosis may mimic anaplasmosis, but one third of patients with ehrlichiosis have a maculopapular or petechial rash, which was not present in this patient. Also, ehrlichiosis is less likely to be associated with thrombocytopenia than is human granulocytic anaplasmosis. On the basis of the constellation of these findings, I overcame my bias toward Covid-19 and considered tickborne infection, particularly anaplasmosis, to be the most likely diagnosis in this patient. To establish this diagnosis, we performed additional testing, including blood testing for Lyme disease antibodies, an examination of thick and thin blood smears for babesia, and nucleic acid testing for A. phagocytophilum DNA. "Most likely diagnosis: Infective Endocarditis - -Differential Diagnosis (ranked by probability): - -1. Infective Endocarditis -2. Lymphoma -3. Acute Hepatitis -4. Disseminated Histoplasmosis -5. Tuberculosis -6. Leukemia -7. Malaria -8. Sarcoidosis -9. Systemic Lupus Erythematosus -10. Rickettsiosis -11. Babesiosis -12. Typhoid Fever -13. Brucellosis -14. Q fever -15. Spleen Lymphoma with Villous Lymphocytes -16. Epstein-Barr Virus Infection -17. Cytomegalovirus Infection -18. Rheumatic Fever -19. Pyogenic Liver Abscess -20. Infectious Mononucleosis." -PMID_34758256-phenopacket-based_query.txt On the basis of the features of the patient’s presentation, the fact that he had been healthy the day before the seizure, and his history of living in a rural area of Guatemala, neurocysticercosis is the most likely diagnosis in this case. To establish this diagnosis, CT was most likely performed, followed by MRI and EEG. "Based on the presented signs and symptoms, my most likely diagnosis is: - -1. Creutzfeldt-Jakob Disease (Prion disease) - -Regarding the differential diagnosis, ordered from the most to least likely: - -1. Creutzfeldt-Jakob Disease (Prion disease) -2. Autoimmune encephalitis (such as Anti-NMDA receptor encephalitis) -3. Neuroleptic malignant syndrome -4. Acute disseminated encephalomyelitis (ADEM) -5. Meningoencephalitis (bacterial, viral, fungal, or parasitic) -6. Status epilepticus -7. Hypoxic-ischemic brain injury -8. Serotonin syndrome -9. Central nervous system vasculitis -10. Systemic Lupus Erythematosus with CNS involvement." -PMID_35476654-phenopacket-based_query.txt Although endomyocardial biopsy may confirm the diagnosis of myocarditis caused by L. monocytogenes , the risks associated with biopsy were thought to outweigh the benefits, so microbial cell-free DNA sequencing was recommended as an alternative diagnostic test. "Most Likely Diagnosis: Antiphospholipid Syndrome (APS) - -Differential Diagnosis (from most likely to least likely): - -1. Antiphospholipid Syndrome (APS) -2. Systemic Lupus Erythematosus (SLE) -3. Chronic Hepatitis C infection -4. Mixed connective tissue disease (MCTD) -5. Multiple Myeloma -6. Behcet's Syndrome -7. Gouty Arthritis with Secondary Hypertension -8. Hyperuricemic Nephropathy -9. Chronic Obstructive Pulmonary Disease (COPD) with Coronary Artery Disease (CAD) -10. Chronic Prostatitis/Chronic Pelvic Pain Syndrome (CP/CPPS) -11. Polymyalgia Rheumatica -12. Rheumatoid Arthritis -13. Non-alcoholic Steatohepatitis (NASH) -14. Chronic Fatigue Syndrome (CFS) -15. Vasculitis -16. Fibromyalgia." -PMID_33626257-phenopacket-based_query.txt Identification of high-grade lymphoma is an unlikely but plausible result. "Most likely diagnosis: Chronic Variable Immunodeficiency (CVID) - -Differential diagnosis: -1. Chronic Variable Immunodeficiency (CVID) -2. Generalized anxiety disorder -3. Seasonal allergic rhinitis -4. Ocular pterygium -5. Post-concussion syndrome -6. Peripheral neuropathy -7. Food allergy leading to anaphylactic shock -8. Subclinical depression -9. Folate deficiency anaemia -10. Ocular migraine -11. Blepharoptosis due to ophthalmic nerve palsy -12. Ocular herpes zoster -13. Ptosis associated with myasthenia gravis -14. Subconjunctival hemorrhage due to high blood pressure -15. T-cell immunodeficiency -16. Post-traumatic stress disorder (PTSD) -17. Multiple Sclerosis (MS) -18. Essential thrombocythemia -19. Glaucoma -20. Secondary immunodeficiency due to medication -21. Chronic fatigue syndrome -22. Major depressive disorder -23. Subconjunctival hemorrhage due to eye injury -24. Subclinical hypothyroidism -25. Seasonal affective disorder -26. Alcoholism -27. Vitamin B deficiency neuropathy -28. Idiopathic intracranial hypertension -29. Dry eye syndrome -30. Episodic cluster headache -31. Subconjunctival hemorrhage related to anticoagulant treatment -32. Central serous retinopathy -33. Systemic lupus erythematosus (SLE) -34. Folic acid deficiency secondary to alcohol abuse -35. Pterygium induced by UV or wind exposure -36. Rare genetic disorders of the immune system." -PMID_35830644-phenopacket-based_query.txt help to refine the differential diagnosis, the definitive test in this case would be a kidney biopsy to establish the cause of the kidney disease. "Based on the given symptoms, my most likely diagnosis is Systemic Lupus Erythematosus (SLE), specifically with Lupus Nephritis, given the presence of granular casts implying kidney involvement. - -My differential diagnoses, ranked by probability, are as follows: - -1. Systemic Lupus Erythematosus (SLE) with Lupus Nephritis -2. Post-streptococcal Glomerulonephritis -3. Goodpasture Syndrome -4. Wegener's Granulomatosis (Granulomatosis with Polyangiitis) -5. Rheumatic Fever -6. Influenza A or B -7. Infectious Mononucleosis -8. Polyarteritis Nodosa -9. Acute Bronchitis -10. Pneumonia -11. Common Cold (Acute Rhinitis) -12. Sinusitis -13. Asthma. -" -PMID_35263523-phenopacket-based_query.txt I recommended repeat MRI of the head with the administration of gadolinium as the next step in the evaluation of this patient. "Most Likely Diagnosis: Late-Onset Parkinson’s disease - -Differential Diagnosis: - -1. Late-Onset Parkinson's Disease -2. Major Depressive Disorder with Psychotic Features -3. Generalized Anxiety Disorder -4. Cardiovascular disease leading to Transient Ischemic Attacks (TIA) or Stroke -5. Alzheimer's disease -6. Chronic Fatigue Syndrome -7. Myasthenia Gravis -8. Primary Immunodeficiency Disorder -9. Hypothyroidism -10. Normal Pressure Hydrocephalus -11. Multiple System Atrophy." -PMID_36383716-phenopacket-based_query.txt carina, and transbronchial needle aspiration was subsequently performed. Dr. Daniel Shepherd: During fine-needle aspiration of the subcarinal mass, a rapid on-site evaluation of the specimen was performed. Hematoxylin and eosin staining (Fig. 3A and 3B) showed clusters of large epithelioid cells with anisonucleosis, irregularly contoured nuclei, prominent nucleoli, and occasional binucleated forms. There was a moderate amount of thin, delicate eosinophilic cytoplasm with occasional intracytoplasmic mucin. These findings are consistent with poorly differentiated adenocarcinoma. No morphologic features of small-cell carcinoma were seen, and immunohistochemical staining for neuroendocrine markers and for programmed death ligand 1 (PD-L1) was negative. Dr. Dudzinski: Radiation and medical oncology management decisions were made. "Most likely diagnosis: Pancreatic Cancer with metastasis - -Differential Diagnosis (Ranked): - -1. Pancreatic cancer with metastasis to lungs -2. Pulmonary embolism secondary to cancer -3. Adenocarcinoma of lung with pancreatic metastasis -4. Mediastinal tumor causing Pancoast syndrome -5. Paraneoplastic syndrome (associated with lung or pancreatic cancer) -6. Neuroendocrine tumor -7. Pericarditis secondary to malignancy -8. Lymphoma with gastrointestinal involvement -9. Progressive metastatic prostate cancer -10. Superior vena cava syndrome secondary to a mediastinal mass. -11. Gastrointestinal stromal tumor with metastasis -12. Autoimmune pancreatitis -13. Lambert-Eaton syndrome (associated with cancer) -14. Von Hippel-Lindau Disease -15. Multiple endocrine neoplasia type-1 (MEN-1) Syndrome -16. Zollinger Ellison Syndrome with secondary complications -17. Idiopathic pulmonary fibrosis with malignancy -18. Primary pleural mesothelioma -19. Thoracic aortic aneurysm with aortic dissection" -PMID_35584159-phenopacket-based_query.txt In pulmonary medicine, we have a saying that “everyone aspirates.” Aspiration can be clinically silent and can occur even in the absence of overt reflux symptoms. The centrilobular nodules and tree-in-bud pattern of opacities seen on this patient’s imaging studies are consistent with aspiration. In addition, this patient had secretions in the airways, mucus plugging, a hiatal hernia, and some residual contrast material in the esophagus, all of which are suggestive of aspiration of oral and gastric contents into the airways. His clinical history, especially the history of GERD and a bitter taste in the mouth, suggests the occurrence of aspiration. This patient’s waxing and waning clinical course would also be consistent with aspiration into the airways. The BAL fluid was notable for acute inflammation and the presence of squamous cells, candida, and bacteria, findings that are consistent with — although not specific for — aspiration of oral contents. Given this presentation, additional testing is warranted. On the basis of this patient’s clinical presentation and radiographic evaluation, infectious and aspiration bronchiolitis are the most likely diagnoses in this case. A thorough microbiologic workup was negative except for the fungal markers. The clinical and radiographic presentations are most consistent with a diffuse aspiration bronchiolitis; however, given this patient’s degree of immunosuppression and positive fungal markers, I would proceed with a lung biopsy to rule out fungal pneumonia and to confirm the diagnosis of aspiration bronchiolitis. "The most likely diagnosis: -Testicular cancer with lung metastasis - -Differential Diagnoses (from most likely to least likely): -1. Testicular cancer with lung metastasis -2. Tuberculosis (extrapulmonary TB) -3. Sarcoidosis -4. Rheumatoid Arthritis associated interstitial lung disease -5. Granulomatosis with polyangiitis -6. Lung cancer with paraneoplastic rheumatological manifestation -7. Lymphoma -8. Metastatic prostate cancer to the lungs -9. Lung abscess due to bacterial pneumonia -10. Legionnaire's disease -11. Chlamydia trachomatis infection causing reactive arthritis and pneumonia." -PMID_34107184-phenopacket-based_query.txt Acquired clotting-factor inhibitor. "Most likely diagnosis: Antiphospholipid syndrome - -Differential diagnosis ranked by probability: -1. Cushing's syndrome -2. Polycythemia vera -3. Atheroembolic disease -4. Paraproteinemic disorders -5. Waldenstrom's macroglobulinemia -6. Hemolytic uremic syndrome -7. Thrombotic thrombocytopenic purpura -8. Systemic lupus erythematosus -9. Diabetes mellitus type 2 -10. Coagulation factor deficiency -11. Chronic venous insufficiency." -PMID_35731657-phenopacket-based_query.txt Despite this patient’s young age and inconclusive evaluation, exocrine pancreatic cancer is the most likely cause of the pancreatic mass. This diagnosis is supported by the persistent soft-tissue mass with a double-duct sign (simultaneous dilatation of the biliary and pancreatic ducts), the persistent stricture of the distal bile duct and obstruction of the biliary and pancreatic ducts, the elevated CA 19-9 levels, and the absence of an alternative diagnosis. "Most Likely Diagnosis: - -Stage IV Metastatic Breast Cancer with gastrointestinal tract involvement - -Robust Differential Diagnosis: - -1. Stage IV Metastatic Breast Cancer with gastrointestinal tract involvement -2. Carcinoid syndrome due to neuroendocrine tumors -3. Pancreatic adenocarcinoma with metastases -4. Metastatic colorectal cancer -5. Hepatic carcinoma with extrahepatic spread -6. Lymphoma (e.g., non-Hodgkin lymphoma) -7. Inflammatory Bowel Disease (IBD), in combination with separate breast carcinoma -8. Mastocytosis, a disorder causing too many mast cells in the body -9. Metastatic malignant melanoma (given the nevus) -10. Wilson disease, a rare genetic disease involving copper metabolism -11. Gaucher disease, a rare genetic disorder leading to the build-up of fatty substances -12. Addison disease, a condition that affects body’s production of adrenal hormones. -13. Paraneoplastic syndromes, like Lambert-Eaton syndrome (which can cause GI symptoms and depression). -14. Widespread metastatic disease of unknown primary origin. -15. Severe Anxiety and Depression (causing somatic symptoms)." -PMID_34936743-phenopacket-based_query.txt but the history does not suggest such an exposure. Because fat droplets are compliant enough to pass through the pulmonary capillary bed and embolize to the central nervous system even in the absence of a patent foramen ovale, the diagnosis of fat embolism syndrome occurring after the liposuction procedure best explains this patient’s combination of lung injury, diffuse alveolar hemorrhage, and cerebral injury. "Likely Diagnosis: -Respiratory Distress Syndrome (ARDS) - -Differential Diagnoses in decreasing order of likelihood: - -1. Pulmonary embolism -2. Acute pneumonia -3. Congestive heart failure -4. Drug overdose (e.g. opioids) -5. Asthmatic attack -6. Sepsis -7. Panhypopituitarism -8. Myocarditis -9. Pulmonary Hypertension -10. Anaphylactic shock -11. Guillain-Barré syndrome -12. Diabetic ketoacidosis-induced respiratory failure." -PMID_33497551-phenopacket-based_query.txt The patient could have primary disseminated tuberculosis, but she is more likely to have reactivation of largely latent disseminated disease in the pleura and CNS as a result of progressive chronic kidney disease, diabetes mellitus, age, and reduced gastric acidity due to gastrectomy. "The following diagnostic test was ordered: Hemoglobin electrophoresis. - -Most Likely Diagnosis: -Amyloidosis, primary (AL) - -Differential Diagnosis, from most likely to least likely: -1. Amyloidosis, primary (AL) -2. Congestive Heart Failure -3. Chronic Kidney Disease -4. Lung Cancer -5. Polycythemia Vera -6. Multiple Myeloma -7. Hemochromatosis -8. Pulmonary Tuberculosis -9. Hypothyroidism -10. Rheumatoid arthritis-associated interstitial lung disease -11. Chronic Obstructive Pulmonary Disorder (COPD) -12. Tubercular Pleural Effusion -13. Pneumococcal Pneumonia -14. Sarcoidosis -15. Systemic Lupus Erythematosus -16. Myasthenia Gravis -17. Parkinson's Disease -18. Lymphoma -19. Cirrhosis -20. Nephrotic Syndrome -21. Atypical pneumonia (Mycoplasma, Legionella) -22. Metastatic Cancer of unknown primary -23. Mitral Valve Disease -24. Pulmonary Hypertension -25. Vasculitis (weeping variant) -26. Goodpasture’s Syndrome -27. Gastrointestinal Stromal Tumor (GIST) -28. Primary Biliary Cirrhosis -29. Endocarditis -30. Diabetic Neuropathy causing autonomic dysfunctions." -PMID_33730458-phenopacket-based_query.txt The absence of radiologic evidence of distant metastatic spread indicated early-stage disease, and an extended right hepatectomy with a Roux-en-Y hepaticojejunostomy was performed with curative intent. Pathological examination of the resection specimen revealed an adenocarcinoma that measured 6.5 cm by 6.5 cm by 6.0 cm, with three satellite nodules that ranged from 0.3 cm to 1.4 cm in diameter. Resection margins were negative but close (<1 mm between the cut margin and the tumor), and three lymph nodes were negative for carcinoma. "Most Likely Diagnosis: -Acute pancreatitis secondary to biliary obstruction due to cholangiocarcinoma. - -Differential Diagnosis: -1. Acute pancreatitis secondary to biliary obstruction due to cholangiocarcinoma -2. Choledocholithiasis leading to acute cholecystitis or acute cholangitis -3. Acute cholecystitis related to cholangiocarcinoma -4. Cholangitis due to biliary obstruction from cholangiocarcinoma -5. Acute peritonitis secondary to perforated peptic ulcer causing acute abdomen and back pain -6. Acute renal colic due to urolithiasis causing back pain -7. Pyelonephritis or other renal pathology causing back pain -8. Spinal disc herniation causing acute back pain -9. Abdominal aortic aneurysm causing back pain -10. Malignant spinal cord compression due to metastasis of cholangiocarcinoma. -11. Pulmonary embolism, presenting with acute abdomen and back pain -12. Acute myocardial infarction, presenting atypically with acute abdomen and back pain." -PMID_34910867-phenopacket-based_query.txt medicines and that the diagnostic test was for a blood lead level. "Most likely diagnosis: -Depression with somatic symptoms - -Differential diagnosis, ranked by probability: - -1. Depression with somatic symptoms -2. Gastric adenocarcinoma -3. Functional dyspepsia -4. Alzheimer's disease -5. Iron deficiency anemia -6. Aphasia due to brain tumor or cerebral metastases -7. Peptic ulcer disease -8. Chronic pancreatitis -9. Generalized anxiety disorder -10. Chronic kidney disease -11. Hypothyroidism -12. Crohn's disease -13. Gastroesophageal reflux disease (GERD) -14. Chronic liver disease -15. Colorectal cancer -16. Non-celiac gluten sensitivity." -PMID_36130001-phenopacket-based_query.txt Inborn error of immunity. "Most likely diagnosis: -Congenital disorders of glycosylation - -Differential diagnoses: -1. Congenital disorders of glycosylation -2. Celiac disease -3. Inflammatory bowel disease -4. Henoch-Schonlein purpura -5. Systemic lupus erythematosus -6. Alport syndrome -7. HIV-associated nephropathy -8. Dense deposit disease -9. Focal segmental glomerulosclerosis -10. IgA nephropathy -11. Minimal change disease -12. Diabetes-induced nephropathy -13. Fabry disease -14. Nephronophthisis." -PMID_34407347-phenopacket-based_query.txt Systemic iron-overload syndrome. "Most Likely Diagnosis: -Hypothyroidism - -Differential Diagnosis: - -1. Hypothyroidism -2. Chronic kidney disease -3. Congestive heart failure -4. Iron deficiency anemia -5. Liver cirrhosis -6. Addison’s disease -7. Rheumatoid arthritis -8. Multiple myeloma -9. Systemic lupus erythematosus -10. Sarcoidosis -11. Chronic obstructive pulmonary disease -12. Melanoma (based on the presence of a nevus) -13. Osteoarthritis (based on knee pain) -14. Polycystic ovary syndrome (although the patient is male, this is included as a differential to consider hormonal imbalances). -15. Diabetes mellitus type 2 -16. Cushing's syndrome -17. Non-Hodgkin Lymphoma -18. Alzheimer's Disease (based on dementia) -19. HIV/AIDS. -20. Pneumocystis jirovecii pneumonia -21. Gout (based on knee pain) -22. Obesity hypoventilation syndrome -23. Congenital adrenal hyperplasia -24. Prostate cancer (considering age and decreased libido) -25. Obstructive sleep apnea." -PMID_35081284-phenopacket-based_query.txt Children with IBD often “fall off” the growth curve long before the diagnosis is made. An early sign of growth failure is a decrease in height velocity. The most likely diagnosis in this patient is IBD. His initial vague gastrointestinal symptoms are atypical of this condition; however, arthralgias and oral aphthous ulcers are both common extraintestinal manifestations. He did not have frankly bloody stools, which could explain why the hemoglobin level was only mildly decreased. The decreased albumin level and mildly elevated lipase level are consistent with a diagnosis of IBD, and the elevated levels of inflammatory markers support the diagnosis. Several features of this patient’s presentation give me pause. Presentation with arthralgias as the dominant symptom and with only mild gastrointestinal symptoms is highly unusual, as is the fact that the most affected joint was his shoulder. Also, he did not have a history of weight loss or growth failure; the absence of these features suggests a recent and rapid onset of illness. Despite his somewhat unusual presentation, I think IBD is the most likely diagnosis in this case. To establish this diagnosis, I would perform colonoscopy and upper endoscopy. "Most likely diagnosis: Juvenile idiopathic arthritis with comorbid Autism Spectrum Disorder - -Differential diagnosis: - -1. Juvenile idiopathic arthritis with comorbid Autism Spectrum Disorder -2. Lupus -3. Hashimoto's thyroiditis with Autism Spectrum Disorder -4. Post-streptococcal reactive arthritis -5. Hyper IgM syndrome -6. HIV/AIDS -7. Lyme disease -8. Tuberculosis -9. Crohn's disease -10. Celiac disease with Autism Spectrum Disorder -11. Chronic Fatigue Syndrome with Autism Spectrum Disorder -12. Central Nervous System Vasculitis -13. Behçet's disease -14. Adult-onset Still's disease. -15. Familial Mediterranean Fever. -16. Sarcoidosis." -PMID_34706175-phenopacket-based_query.txt Although this patient did not have evidence of leukemic cells on oral biopsy, the diagnosis of leukemia would account for his weight loss, worsening ulcers that did not respond to therapy, and increasing eosinophilia despite treatment with glucocorticoids. To establish the diagnosis in this case, I would recommend a bone marrow biopsy. "Based on the provided case, my most likely diagnosis is Sezary Syndrome with underlying Diabetes Mellitus and Prostate Cancer. - -Here is my differential diagnosis, ranked from most to least likely: - -1. Sezary Syndrome -2. Diabetes Mellitus Type 2 -3. Prostate Cancer -4. Bullosis Diabeticorum -5. Behcet's Syndrome -6. Rheumatoid Arthritis -7. Gastroesophageal Reflux Disease -8. Alcoholic Liver Disease -9. Pityriasis Lichenoides Chronica -10. Langerhans Cell Histiocytosis -11. Hyper IgM Syndrome -12. Pyoderma Gangrenosum -13. Chronic Actinic Dermatitis -14. Coeliac Disease -15. Spondylitis -16. HIV infection with secondary opportunistic infection -17. Other type of sexually transmitted disease -18. Acute graft-versus-host-disease. -" -PMID_33852783-phenopacket-based_query.txt In summary, this patient’s presentation with regional tender lymphadenopathy and history of exposure to cats makes cat scratch disease the most likely diagnosis in this case. An atypical presentation of a systemic infection, a systemic granulomatous process such as sarcoidosis, and lymphoproliferative disorder cannot be ruled out. To establish the diagnosis, I would recommend a right inguinal lymph-node biopsy and serologic testing for B. henselae and other infectious causes. "Based on these symptoms, my most likely diagnosis would be: - -1. Systemic Lupus Erythematosus - -Differential Diagnosis list, ranked from most likely to least likely: - -1. Systemic Lupus Erythematosus -2. HIV/ AIDS -3. Common Variable Immunodeficiency -4. Sarcoidosis -5. Tuberculosis -6. Crigler-Najjar Syndrome -7. Addison's disease -8. Chronic Kidney Disease -9. Vibrio vulnificus infection -10. Hashimoto's thyroiditis -11. Multiple Sclerosis -12. Neurosyphilis -13. Erdheim-Chester Disease -14. Wilson's Disease -15. Myelodysplastic syndromes." -PMID_33979492-phenopacket-based_query.txt Hemophagocytic lymphohistiocytosis. "Given the symptoms and test results presented, the most likely diagnosis is Paraneoplastic syndrome due to lung cancer. - -Here is my differential diagnosis in order of probability: - -1. Paraneoplastic syndromes due to lung cancer -2. B-cell lymphoma -3. Multiple myeloma -4. Metastatic carcinoma -5. Sezary syndrome -6. Hodgkin lymphoma -7. Iron-deficiency anemia -8. Chronic hepatic disease -9. Endocarditis -10. Gastric lymphoma." -PMID_36070713-phenopacket-based_query.txt Thus, the negative test result does not dissuade me from making a diagnosis of candida meningitis. I suspect the diagnostic test was a CSF fungal culture. "Based on the given clinical picture, my most likely diagnoses is: Pseudotumor cerebri (Idiopathic Intracranial Hypertension) - -For the differential diagnosis: -1. Pseudotumor cerebri (Idiopathic Intracranial Hypertension) -2. Malignant Hypertension -3. Benign Intracranial Hypertension -4. Pituitary tumour causing hyperprolactinemia -5. Space-occupying lesions in Central Nervous System (like brain tumour) -6. Ovarian cancer with brain metastasis -7. Arnold-Chiari Malformation -8. Meningitis/Encephalitis -9. Intracranial vascular lesions (like aneurysms) -10. Cavernous sinus thrombosis -11. Multiple sclerosis -12. Acute angle-closure glaucoma -13. Neurosyphilis -14. Retrobulbar neuritis -15. Optic neuritis -16. Migraine-associated ophthalmoplegia. -17. Leptomeningeal metastasis" -PMID_34587390-phenopacket-based_query.txt The findings on echocardiography in this case ruled out aneurysm involving the ascending aorta or aortic root. In view of all these factors and the overall frequency at which these mutations arise in the population, the most likely genetic diagnosis in this patient, who had recurrent dissection of medium-sized arteries and joint dysfunction in the absence of thoracic aortic aneurysm, is the vascular form of Ehlers–Danlos syndrome, which is caused by mutations in COL3A1 . "Based on the presented symptoms, my most likely diagnosis is Migraines. - -For the differential diagnosis, ranked on the basis of their probability, is as follows: - -1. Migraines -2. Middle Ear Infection -3. Meniere's disease -4. Vestibular Neuronitis -5. Transient Ischemic Attack (TIA) -6. Acoustic Neuroma -7. Labyrinthitis -8. Multiple Sclerosis -9. Cerebral Aneurysm -10. Brain Tumour -11. Hypertension -12. Diabetic Neuropathy -13. Postural orthostatic tachycardia syndrome (POTS) -14. Motion sickness." -PMID_35443111-phenopacket-based_query.txt Systemic lupus erythematosus. "Most Likely Diagnosis: -1. Guillain-Barre Syndrome - -Differential Diagnosis: -1. Guillain-Barre Syndrome -2. Myasthenia Gravis -3. Multiple Sclerosis -4. Bell's Palsy -5. Stroke -6. Brain tumor -7. Amyotrophic Lateral Sclerosis (ALS) -8. Lyme disease -9. Botulism -10. Neurosarcoidosis -11. Systemic Lupus Erythematosus (SLE) -12. Metabolic myopathies -13. Hypothyroidism -14. Sarcoidosis -15. Meningitis -16. Encephalitis -17. Wilson's Disease -18. Vasculitis affecting central nervous system -19. Mitochondrial myopathies -20. Hypokalemic periodic paralysis -21. Hyperkalemic periodic paralysis -22. Conversion Disorder -23. Paraneoplastic Syndrome." -PMID_36001715-phenopacket-based_query.txt If specimens obtained during bronchoscopy are nondiagnostic, then lung biopsy by means of video-assisted thoracoscopic surgery should be performed. "Most Likely Diagnosis: -Acute Pancreatitis - -Differential Diagnosis: -1. Acute Pancreatitis -2. Peptic Ulcer Disease -3. Cholecystitis -4. Gastritis -5. Gastroenteritis -6. Gastroesophageal Reflux Disease (GERD) -7. Gallstones -8. Gastric Cancer -9. Hepatitis -10. Appendicitis -11. Abdominal Aortic Aneurysm -12. Myocardial Infarction -" -PMID_34133863-phenopacket-based_query.txt However, in clinical medicine, patient presentations often do not fit these maxims, and this is one clinical situation in which a life-threatening diagnosis — acute pulmonary embolism — must be ruled out. Therefore, in addition to testing the patient’s nasopharyngeal specimen for SARS-CoV-2 RNA to establish the diagnosis of Covid-19, I would recommend obtaining a computed tomographic (CT) pulmonary angiogram to identify pulmonary embolism. "Most Likely Diagnosis: -Pneumonia - -Differential Diagnoses: - -1. Pneumonia -2. Chronic obstructive pulmonary disease (COPD) exacerbation -3. Congestive heart failure (CHF) -4. Pulmonary embolism -5. Myocardial infarction (MI) -6. Lung cancer -7. Tuberculosis -8. Pulmonary edema -9. Pleurisy -10. Acute bronchitis -11. Atelectasis -12. Pulmonary fibrosis." -PMID_35196431-phenopacket-based_query.txt mellitus, acute hyperglycemia with ketosis is a common first presentation; subsequently, betacell destruction leads to absolute insulin deficiency. By contrast, patients with syndromes of insulin resistance and relative insulin deficiency rarely present with ketosis. It is worth noting that this patient, despite his elevated anion gap and serum ketone level, did not have acidemia. However, the venous blood gas analysis and serum bicarbonate level are consistent with an excess of bicarbonate, suggesting that a concurrent metabolic alkalosis (of unclear cause) kept the serum pH in a normal range. In this patient, who had an acute presentation with new hyperglycemia and associated ketosis, autoimmune diabetes is the leading diagnosis. Patients with classic type 1 diabetes mellitus typically first present during childhood or adolescence, and this patient was 68 years of age at symptom onset. Pembrolizumab treatment is his most compelling risk factor for newonset autoimmune diabetes; I suspect that the diagnosis is ICI-induced diabetes. There is no definitive diagnostic test to confirm this diagnosis, but it would be helpful to check blood levels of glycated hemoglobin, islet-cell autoantibodies, and — after treatment with insulin and stabilization of blood glucose levels — C-peptide. "Most Likely Diagnosis: -Metastatic Melanoma - -Differential Diagnosis: -1. Progression of superficial spreading melanoma with brain metastasis - This could account for the reported seizure and slurred speech. -2. Paraneoplastic syndrome associated with melanoma - Causes symptoms such as weight loss and fatigue, and in some cases, neurological manifestations like seizures. -3. Hypothyroidism - The patient’s fatigue and weight gain might be due to the hypothyroid status. -4. Neurodegenerative disorder (eg, Parkinson’s disease) - Slurred speech and seizures can be an indication. -5. Autoimmune Disorder - Certain autoimmune disorders can lead to seizures, slurred speech, hypothyroidism, and fatigue. -6. Hyperlipidemia-induced Atherogenic Cerebrovascular Disease - Could possibly cause neurological symptoms like seizures and slurred speech. -7. Multiple system atrophy - Neurodegenerative disease that can include a combination of parkinsonism, cerebellar ataxia, and autonomic malfunction. This might explain the nocturia, slurred speech, and seizures. -8. Side effects of medications - These can cause a wide array of symptoms including fatigue, weight loss, seizures, and slurred speech. -9. Advanced age-related multi-systemic dysfunction - An array of multiple systemic problems associated with aging could be causing the constellation of signs and symptoms. -10. Vasculitis - Could cause seizures, slurred speech due to hypothyroidism, fatigue and weight loss. -11. Lyme disease - Marked by fatigue, possible neurological manifestations. -12. Tuberculosis or other opportunistic infections - Given the presence of a malignant condition (melanoma), these should be considered, as they can cause weight loss and fatigue." -PMID_33882209-phenopacket-based_query.txt Varicella–zoster virus infection. "Most likely diagnosis: Paraneoplastic syndrome associated with testicular cancer, such as a gonadotropin-secreting germ cell tumor. - -Differential diagnosis: -1. Testicular cancer with associated paraneoplastic syndrome -2. Lymphoma with paraneoplastic syndrome -3. Klinefelter syndrome -4. Immunodeficiency diseases like HIV/AIDS -5. Age-related diseases like benign prostatic hyperplasia, cataract, and macular degeneration -6. Allergic responses possibly leading to conjunctival hyperemia, chemosis, allergic rhinitis, and skin rash -7. Depression due to chronic diseases and age -8. Cutaneous side effect due to cancer treatments -9. Other neoplastic diseases like skin cancer -10. Advanced age-related conditions with multiple comorbidities." -PMID_34379926-phenopacket-based_query.txt to HIV occurred 3 weeks before hospital admission, the patient would be likely to have a detectable HIV RNA viral load and detectable HIV p24 antigen and may have detectable HIV-1 or HIV-2 antibodies; approximately 30% of patients with acute HIV infection have evidence of an evolving antibody response. "Most likely diagnosis: -Lyme Neuroborreliosis - -Differential diagnosis: -1. Lyme Neuroborreliosis -2. Multiple Sclerosis -3. Polymyositis -4. Subacute Bacterial Endocarditis -5. Hypothyroidism -6. Meningitis -7. Encephalitis -8. Guillain-Barré Syndrome -9. Autoimmune Encephalitis -10. Primary Central Nervous System Lymphoma -11. Secondary Metastasis to Brain -12. Myasthenia Gravis -13. Metabolic Encephalopathy -14. Normal Pressure Hydrocephalus -15. Creutzfeldt-Jakob Disease -16. West Nile Encephalitis -17. Tuberculosis -18. HIV-related cognitive impairment." -PMID_35417641-phenopacket-based_query.txt For this reason, I think that the schistocytes are a “red herring” in this case that biased the initial diagnosis toward a destructive process such as TTP, rather than a production problem such as MDS. Overall, this patient’s history and current presentation are consistent with progression of MDS. I suspect that the diagnostic test was a repeat bone marrow biopsy with cytogenetic analysis and next-generation sequencing. "The most likely diagnosis: -Thrombotic Thrombocytopenic Purpura (TTP) - -Differential diagnoses, ranked by likelihood: -1. Thrombotic Thrombocytopenic Purpura (TTP) -2. Hemolytic Uremic Syndrome (HUS) -3. Myelodysplastic syndrome (MDS) -4. Atypical Hemolytic Uremic Syndrome (aHUS) -5. Disseminated Intravascular Coagulation (DIC) -6. Autoimmune Hemolytic Anemia (AIHA) -7. Severe Sepsis -8. Gastrointestinal Stromal Tumor (GIST) -9. Paroxysmal Nocturnal Hemoglobinuria (PNH) -10. Leukemia -11. Lymphoma" -PMID_33913642-phenopacket-based_query.txt Dr. Dorit Koren’s Initial Diagnosis "This case presentation is not sufficient to provide a diagnosis. The only notable factor is maternal diabetes, which indicates that the infant belongs to a mother who has diabetes. This can cause risks and complications for the newborn such as macrosomia, neonatal hypoglycemia, or birth trauma. However, without any other symptoms, specific signs, or further details, it is not possible to provide a diagnosis or an appropriate differential diagnosis. It is crucial to have specific symptoms, clinical findings, and information about physical examination, personal history, and family history to propose a reliable diagnosis." -PMID_35172059-phenopacket-based_query.txt The rapidity of this patient’s disease progression, combined with the known diagnosis of Creutzfeldt–Jakob disease in her father, are highly suggestive of a genetic form of Creutzfeldt–Jakob disease. "Most Likely Diagnosis: Multiple Sclerosis - -Differential Diagnosis: -1. Multiple Sclerosis -2. Cerebrovascular Disease -3. Spinocerebellar Ataxia -4. Cervical Spondylosis with Myelopathy -5. Brain Tumor -6. Acoustic Neuroma -7. Chronic Inflammatory Demyelinating Polyneuropathy -8. Huntington's Disease -9. Glaucoma (for blindness) -10. Neurosyphilis -11. Wernicke's Encephalopathy" -PMID_33471980-phenopacket-based_query.txt leaving us with two possible diagnoses: myocarditis or a large myocardial infarction. When all the features of this patient’s presentation are considered, her primary diagnosis was most likely biventricular cardiomyopathy due to either myocarditis or pregnancy-associated myocardial infarction. Owing to the severity of the ventricular dysfunction, a myocardial infarction would have probably involved the left main coronary artery or multiple coronary arteries. To further refine the differential diagnosis, I would recommend coronary angiography to evaluate the coronary arteries and, if possible, native endomyocardial biopsy, recognizing that the patient is currently receiving anticoagulation for the ECMO circuit. "Most likely diagnosis: - -Peripartum cardiomyopathy - -Differential Diagnosis (from most likely to least likely): - -1. Peripartum cardiomyopathy -2. Viral myocarditis -3. Idiopathic dilated cardiomyopathy -4. Rheumatic heart disease -5. Congestive heart failure due to unrecognized congenital heart disease -6. Arrhythmogenic right ventricular cardiomyopathy/dysplasia -7. Systemic lupus erythematosus-induced cardiomyopathy -8. Sarcoidosis-induced cardiomyopathy -9. Thyroid-induced cardiac failure -10. Ischemic cardiomyopathy due to coronary artery embolism -11. Pulmonary hypertension due to unrecognized chronic lung disease." -PMID_34161710-phenopacket-based_query.txt To establish the diagnosis of delayed posthypoxic leukoencephalopathy, I would recommend performing magnetic resonance imaging (MRI) of the head with attention to the T2-weighted fluid-attenuated inversion recovery (FLAIR) sequences. "Most likely diagnosis: Paraneoplastic neurological syndrome secondary to squamous cell carcinoma of the tongue - -Differential Diagnosis (from most likely to least likely): - -1. Paraneoplastic neurological syndrome secondary to squamous cell carcinoma of the tongue -2. Metastatic squamous cell carcinoma (brain metastasis) -3. Central nervous system infection (like meningitis or encephalitis) -4. Neurodegenerative disorders (such as Alzheimer's or Parkinson's disease) -5. Hypoxic-ischemic encephalopathy (secondary to aspiration pneumonia) -6. Hyperactive delirium secondary to acute medical illness -7. Cervical Spondylosis causing cervical myelopathy -8. Myasthenia gravis -9. Guillain-Barre syndrome -10. Multiple Sclerosis -11. Alcohol-related brain damage -12. Vitamin B12 deficiency neuropathy -13. Critical illness polyneuropathy/myopathy -14. Hypothyroidism causing peripheral neuropathy -15. Conversion disorder -16. Vascular dementia due to chronic ischemia -17. Neurosyphilis." -PMID_34320292-phenopacket-based_query.txt Dr. Olivia C. Smibert’s Diagnosis "Considering the symptoms, my most likely diagnosis is: - -Primary Systemic AL Amyloidosis - -Here's a list of potential diagnoses ranked by likelihood: - -1. Primary Systemic AL Amyloidosis -2. Multiple Myeloma -3. Henoch-Schonlein Purpura -4. Granulomatosis with Polyangiitis (GPA) -5. Systemic Lupus Erythematosus -6. Thrombotic Thrombocytopenic Purpura -7. Microscopic Polyangiitis -8. Polyarteritis Nodosa -9. Essential Thrombocythemia -10. Goodpasture Syndrome -11. Behcet Syndrome -12. Sjogren Syndrome -13. Paroxysmal Nocturnal Hemoglobinuria." -PMID_35613025-phenopacket-based_query.txt This patient meets all consensus diagnostic criteria for iMCD except for the histologic features in lymph node tissue, so a second review of the specimen is warranted. "The most likely diagnosis: Lymphoma, possibly Non-Hodgkin Lymphoma - -Differential diagnoses, ranked by likelihood: -1. Non-Hodgkin Lymphoma -2. Sarcoidosis -3. Systemic Lupus Erythematosus -4. Infectious mononucleosis -5. Tuberculosis -6. Mediastinal Carcinoma (e.g. Lung cancer, Thymoma) -7. Granulomatosis with polyangiitis (Wegener's granulomatosis) -8. Q fever -9. Whipple's disease -10. Castleman's disease -11. Invasive fungal infections (e.g. Histoplasmosis, Aspergillosis) -12. HIV/AIDS related conditions -13. Lyme Disease -14. Mycobacterium avium complex (MAC) infection -15. Hodgkin's lymphoma -16. Leukemia -17. Paraneoplastic syndromes -18. Adult-onset Still's disease -19. Mast cell activation syndrome -20. Acute infectious mononucleosis -21. Behcet's disease" -PMID_33503346-phenopacket-based_query.txt If the diagnosis of primary amyloidosis is confirmed in this patient, I would also recommend a bone marrow biopsy to rule out multiple myeloma, which occurs in 10 to 15% of patients with primary amyloidosis. "Here is my response based on the provided case details: - -Most Likely Diagnosis: -1. Paraneoplastic syndrome related to Breast Carcinoma presenting with Lambert-Eaton Myasthenic Syndrome (LEMS) - -Differential Diagnosis Ranked by Probability: -1. Anti-Yo Paraneoplastic Encephalitis (a type of Paraneoplastic Neurological Syndrome) -2. Sjogren's syndrome with secondary fibromyalgia -3. Multiple Sclerosis Plexopathy -4. Giant Cell Arteritis -5. Antiphospholipid Syndrome -6. Subacute Cutaneous Lupus Erythematosus -7. Myasthenia Gravis -8. Polymyalgia Rheumatica -9. Fibromuscular Dysplasia -10. Rheumatoid Arthritis -11. Systemic Vasculitis. - -I trust that the confirmatory tests will help validate these diagnoses." -PMID_35020988-phenopacket-based_query.txt The reported response rate to immunotherapy ranges from 10 to 70%. Combination therapy seems to be more effective than monotherapy. This patient had many of the typical sleep symptoms reported in patients with anti-IgLON5 disease, as well as a combination of neurologic symptoms reported in patients with clinical subtypes of the disease. To establish this diagnosis, testing for IgLON5 autoantibodies was performed. "From the information provided, my most likely diagnosis is Amyotrophic Lateral Sclerosis (ALS). - -My differential diagnoses, in order of probability from the most likely to the least likely are: - -1. Amyotrophic Lateral Sclerosis (ALS) -2. Progressive Bulbar Palsy -3. Multiple System Atrophy -4. Primary Lateral Sclerosis -5. Bulbar onset Myasthenia Gravis -6. Brainstem stroke -7. Progressive Supranuclear Palsy -8. Parkinson's Disease -9. Multiple Sclerosis -10. Spinocerebellar Ataxia." -PMID_36351271-phenopacket-based_query.txt I suspect that this patient had neuroinflammation associated with Covid-19 that contributed to depression, catatonia, and Cotard’s syndrome. "Most Likely Diagnosis: Alzheimer's disease associated with comorbidity of Mixed anxiety-depressive disorder - -Differential Diagnosis: -1. Alzheimer's Disease -2. Mixed anxiety-depressive disorder -3. Gastroesophageal reflux disease (GERD) -4. Chronic Obstructive Pulmonary Disease (COPD) -5. Hereditary angioedema -6. Major Depressive Disorder -7. Essential hypertension -8. Obesity due to excess calories -9. Chronic bronchitis -10. Chronic pharyngitis -11. Myalgic Encephalomyelitis (Chronic Fatigue Syndrome) -12. Insomnia due to mental disorder." -PMID_34879452-phenopacket-based_query.txt Approximately 50% of cases are associated with oral ulcers, often on the tongue. The arthralgias, fever, presence of anti-Ro antibodies, abnormal results on liverfunction tests, and elevated ferritin level seen in this patient are common in patients with anti– MDA-5 dermatomyositis. I suspect that the most likely diagnosis in this patient is anti–MDA-5 dermatomyositis. To establish this diagnosis, I would review the results of the muscle biopsy and test for antibodies directed against myositis-associated autoantigens, including MDA-5. "Most likely diagnosis: Metastatic Neoplasia/ Cancer with Multiple Primary Sites. - -Differential Diagnoses: -1. Metastatic Neoplasia/Cancer with Multiple Primary Sites -2. Autoimmune Disease such as Systemic Lupus Erythematosus -3. Paraneoplastic Syndrome -4. Multiple Myeloma or another hematological malignancy -5. Behçet's Disease -6. Polymyalgia Rheumatica -7. Tuberculosis -8. Secondary Syphilis -9. HIV/AIDS-related opportunistic infections or malignancies -10. Hypereosinophilic Syndrome." -PMID_33596360-phenopacket-based_query.txt Disseminated bacille Calmette–Guérin infection. "Most Likely Diagnosis: -Non-Hodgkin's Lymphoma. - -Differential Diagnoses: -1. Chronic lymphocytic leukemia -2. Multiple myeloma -3. Hodgkin's lymphoma -4. Acute myeloid leukemia -5. Liver cirrhosis secondary to alcoholic liver disease -6. Liver cirrhosis secondary to viral hepatitis -7. Gaucher's disease -8. Tuberculosis -9. Sarcoidosis -10. Metastatic cancer" -PMID_34670047-phenopacket-based_query.txt available, including radionuclide scanning (with the use of technetium-99m–labeled sestamibi), dynamic CT, magnetic resonance imaging, and ultrasonography. I would opt for ultrasonography in this young patient in order to avoid exposure to the radiation that is inherent with CT and radionuclide scans. How does the finding of hyperparathyroidism influence the diagnosis of the mandibular mass? The possibility of the diagnosis of an atypical ossifying fibroma is increased, given its occurrence in the context of hyperparathyroidism due to CDC73 mutations. Nevertheless, brown tumors are a complication of hyperparathyroidism, and the reported biopsy and radiographic findings are more consistent with this type of lesion. "I'm sorry, but the case you provided is incomplete. It says a 14-year old female presented with signs and symptoms but doesn't specify what those signs and symptoms were. I cannot provide a diagnosis or a differential diagnosis based on this information. Can you please provide full details of the case?" -PMID_36546630-phenopacket-based_query.txt Hepatic adenoma. "Most likely diagnosis: -Chronic Granulomatous Disease - -Differential diagnosis: -1. Chronic Granulomatous Disease -2. HIV/AIDS -3. Lupus (Systemic Lupus Erythematosus) -4. Multiple Sclerosis -5. Immunoglobulin A Deficiency -6. Common variable immunodeficiency -7. X-linked agammaglobulinaemia -8. CVID (Common Variable Immune Deficiency) -9. Specific antibody deficiency -10. Cervical Cancer -11. Polycystic Ovary Syndrome -12. Renal Cell Carcinoma -13. Kidney stones (Nephrolithiasis) -14. Hepatitis B or C -15. Hepatocellular carcinoma -16. Pyelonephritis -17. Tuberculosis -18. Sarcoidosis -19. PID (Pelvic inflammatory disease) -20. Gastroenteritis -21. Functional dyspepsia -22. Gastritis -23. Peptic ulcer" -PMID_35704485-phenopacket-based_query.txt Unfortunately, diagnosis is often delayed, and patients may be wheelchair-bound or bedbound by the time of diagnosis. The tumor can be found almost anywhere in the body, is usually benign, and can be removed or ablated, although it can recur years later. Tumor-induced osteomalacia is the most likely diagnosis in this patient. I suspect that the diagnostic test was assessment for an elevated blood level of FGF23, followed by imaging studies to identify a tumor. It is prudent to make a biochemical or genetic diagnosis of tumor-induced osteomalacia before performing imaging studies, because the tumor can occur anywhere in the body and false positive imaging studies are common. "The most likely diagnosis is: - -Tumor-Induced Osteomalacia (TIO) - -Here are the ranked differential diagnoses: - -1. Tumor-Induced Osteomalacia (TIO) -2. X-Linked Hypophosphatemia (XLH) -3. Vitamin D Deficiency Rickets (adult form) -4. Chronic Kidney Disease (mineral and bone disorder) -5. Fanconi Syndrome -6. Autosomal Dominant Hypophosphatemic Rickets (ADHR) -7. Autosomal Recessive Hypophosphatemic Rickets (ARHR) -8. Fibrous Dysplasia -9. Hyperparathyroidism -10. Osteogenesis Imperfecta." -PMID_33567196-phenopacket-based_query.txt To establish this diagnosis, I would recommend performing a lung biopsy. "The most likely diagnosis: Churg-Strauss Syndrome (eosinophilic granulomatosis with polyangiitis) - -Differential diagnoses, listed from most likely to least likely: - -1. Churg-Strauss Syndrome -2. Gastroesophageal reflux disease (GERD) with associated chronic bronchitis -3. Asthma -4. Allergic rhinitis and conjunctivitis with secondary infection -5. Chronic obstructive pulmonary disease (COPD) -6. Atopic dermatitis (cause of eczema) -7. Systemic lupus erythematosus (SLE, possible cause of positive antinuclear antibody test) -8. Sarcoidosis -9. Pulmonary fibrosis -10. Surreptitious diuretic use -11. Pneumoconiosis -12. Bronchiectasis -13. Hypereosinophilic syndrome." -PMID_36239648-phenopacket-based_query.txt both gastric accommodation and gastric emptying. Progressive disease can lead to gastric-outlet obstruction. Because the liver is the common venous drainage point for most of the gastrointestinal tract, it is a frequent site of hematogenous metastases, which appear as hypodense lesions on CT. This patient initially had breakthrough heartburn that did not respond to previously effective acid-suppression therapy, which could represent malignant infiltration of the clasplike sling fibers that originate from the upper stomach and form part of the normal acid barrier. Malignant infiltration of the submucosal and muscularis propria layers of the fundus impairs normal gastric accommodation, which leads to early satiation. Malignant infiltration of the entire antral wall disrupts the neurocircuitry and muscular contractions that are required for gastric emptying. This process initially mimics gastroparesis, with retention of solid food and nausea, but prokinetic treatments are ineffective because damage to the muscularis propria prevents these agents from effectively triggering antral contractions. Liquids are initially tolerated because they are emptied passively. However, progressive antral disease marks a transition from gastroparesis to gastric-outlet obstruction, and liquids are no longer tolerated. Patients with linitis plastica frequently present with advanced disease, and this patient’s hypodense liver lesions may suggest metastatic disease. Given this patient’s rapidly progressive symptoms that are suggestive of specific alterations in gastric physiology, in combination with his imaging and EGD findings, I favor a diagnosis of gastric cancer that is consistent with linitis plastica. The diagnostic test of choice would be endoscopic ultrasonography (EUS). "Most likely diagnosis: -Parkinson’s Disease (gastrointestinal manifestations) - -Robust Differential Diagnosis (ranked by probability from most to least likely): -1. Idiopathic Gastroparesis -2. Autonomic Neuropathy (particularly Diabetic Autonomic Neuropathy) -3. Chronic Intestinal Pseudo-obstruction -4. Medication-induced constipation and gastroparesis -5. Systemic sclerosis (Scleroderma) -6. Amyloidosis -7. Multiple system atrophy -8. Paraneoplastic syndrome related gastrointestinal issues -9. Fabry Disease -10. Mitochondrial neurogastrointestinal encephalopathy (MNGIE) -" -PMID_36416771-phenopacket-based_query.txt Optic nerve tumor, either optic nerve sheath meningioma or optic nerve glioma. "Most likely diagnosis: -Neurocutaneous Syndromes (specifically Tuberous Sclerosis Complex) - -Differential Diagnosis: -1. Neurocutaneous Syndromes (Tuberous Sclerosis Complex) -2. Systemic Lupus Erythematosus -3. Multiple Sclerosis -4. Vogt-Koyanagi-Harada Disease -5. Albinism (Oculocutaneous Type) -6. Sarcoidosis -7. Behcet’s Disease -8. Myasthenia Gravis -9. Optic Nerve Glioma -10. Sturge-Weber Syndrome -11. Neuromyelitis Optica (Devic’s Syndrome) -12. Neurofibromatosis -13. Hypomelanosis of Ito." -PMID_35939582-phenopacket-based_query.txt tory, and duration of symptoms are most consistent with a diagnosis of insulinoma. To establish this diagnosis, I would initiate a supervised fast to monitor for symptomatic hypoglycemia. In addition, I would measure serum levels of glucose, insulin, C-peptide, proinsulin, and β-hydroxybutyrate. "Most Likely Diagnosis: -Insulinoma - -Differential Diagnosis: -1. Insulinoma -2. Adrenal insufficiency -3. Hypopituitarism -4. Factitious hypoglycemia (Self-Administered Insulin or Anti-Diabetic Drugs) -5. Surreptitious sulfonylurea ingestion -6. Non-islet cell tumor hypoglycemia -7. Alcohol consumption related hypoglycemia -8. Reactive hypoglycemia -9. Postprandial syndrome (dumping syndrome) -10. Prader-Willi syndrome." -PMID_36300978-phenopacket-based_query.txt Sarcoidosis or tuberculosis. "Most likely diagnosis: Juvenile Idiopathic Arthritis-associated Uveitis - -Differential Diagnosis: -1. Juvenile Idiopathic Arthritis-associated Uveitis -2. Systemic Lupus Erythematosus -3. Behçet’s disease -4. Sarcoidosis -5. Endogenous Endophthalmitis -6. Kawasaki disease -7. Lymphoma involving the eye -8. Viral retinitis -9. Acute Retinal Necrosis -10. Tuberculosis-associated uveitis -11. Fungal endophthalmitis -12. Retinopathy due to pediatric hypertension -13. Syphilis-related eye disease -14. Orbital Cellulitis -15. Secondary glaucoma due to uveitis -16. Lyme disease-related uveitis." -PMID_34644476-phenopacket-based_query.txt death and a very low chance of recovery without urgent treatment and consideration of bone marrow transplantation. "Based on this case, my most likely diagnosis is: - -Platelet function disorder due to hyperlipidemia-induced aplastic anemia. - -The list of differential diagnoses, ranked by their probability is as follows: - -1. Platelet function disorder due to hyperlipidemia-induced aplastic anemia. -2. Vitamin C deficiency (Scurvy) presenting with skin and mucous membrane signs. -3. Hereditary hemorrhagic telangiectasia, a rare genetic disorder causing bleeding problems. -4. Wiskott-Aldrich Syndrome - a rare X-linked recessive disease characterized by eczema, thrombocytopenia (low platelet count), autoimmune disorders, and an increased risk of malignancy. -5. Systemic lupus erythematosus, an autoimmune disease with clinical presentation of oral ulcers and thrombocytopenia. -6. Immune thrombocytopenic purpura, a bleeding disorder in which the blood doesn't clot as it should because of a low number of blood cell fragments called platelets. -7. Pseudothrombocytopenia due to EDTA interference, a currently rare artifact of blood sample analysis. -8. Bernard-Soulier Syndrome, a disorder of platelet adhesion. -9. Glanzmann thrombasthenia, a disorder of platelet aggregation. -10. Essential thrombocytosis, a rare chronic blood disorder characterized by the overproduction of platelets by megakaryocytes in the bone marrow. -11. Hemophilia, a group of inherited blood disorders in which the blood does not clot properly. -12. Von Willebrand Disease, a bleeding disorder caused by a deficiency of Von Willebrand factor, a molecule that helps platelets adhere to damaged endothelium. -13. Platelet storage pool deficiency, a condition in which there is a deficiency of dense granules in the platelets." -PMID_34233100-phenopacket-based_query.txt In this patient with the triad of cerebellar ataxia, neuropathy, and bilateral vestibular dysfunction, the clinical syndrome of CANVAS is the most likely diagnosis. Given the patient’s family history of a shuffling gait and celiac disease, immune and genetic causes of this syndrome should be ruled out. "Most Likely Diagnosis: -Multiple System Atrophy (MSA) - -Differential Diagnosis: -1. Multiple System Atrophy (MSA) -2. Parkinson's Disease -3. Cerebrovascular Disease -4. Diabetic Autonomic Neuropathy -5. Normal Pressure Hydrocephalus -6. Progressive Supranuclear Palsy -7. Lewy Body Dementia -8. Spinocerebellar Ataxia -9. Vascular Parkinsonism -10. Metabolic or Nutritional Disorders such as vitamin B12 deficiency -11. Creutzfeldt-Jakob Disease" -PMID_36516093-phenopacket-based_query.txt Because of the need to rule out adrenocortical carcinoma, laparoscopic right adrenalectomy was performed. "Based on the case details, the most likely diagnosis is: -1. Li-Fraumeni syndrome - -Robust differential diagnosis, ranked by their probability are as follows: -1. Li-Fraumeni syndrome -2. Cowden syndrome -3. Peutz-Jeghers syndrome -4. Neurofibromatosis type 1 -5. Familial Adenomatous Polyposis -6. Lynch syndrome -7. Multiple endocrine neoplasia type 1 (MEN1) -8. Multiple endocrine neoplasia type 2 (MEN2) -9. Hereditary nonpolyposis colorectal cancer (HNPCC) -10. Werner syndrome -11. Hereditary breast and ovarian cancer syndrome." -PMID_35704401-phenopacket-based_query.txt terms “poxvirus,” “outbreak,” and “sexually transmitted infection” revealed a report that had been posted on the same day by public health authorities in the United Kingdom. It described four cases similar to this one, in which a diagnosis of monkeypox had been confirmed. It was at this point that I contacted the infection control unit at our hospital to report my concern that the patient may have monkeypox. "Most likely diagnosis: -HIV/AIDS with secondary Acute Retroviral Syndrome - -Differential Diagnosis: -1. HIV/AIDS with secondary Acute Retroviral Syndrome -2. Secondary Syphilis -3. Acute Infectious Mononucleosis -4. Human Herpesvirus 6 (HHV-6) Infection -5. Acute Lymphocytic Leukemia -6. Hodgkin's Lymphoma -7. Non-Hodgkin's Lymphoma -8. Graft-versus-host disease (Post-transplant) -9. Systemic Lupus Erythematosus -10. Acute Myeloid Leukemia -11. Sarcoidosis -12. Tuberculosis. -13. Behçet's disease -14. Kikuchi disease -15. Adult-onset Still's disease" -PMID_34010534-phenopacket-based_query.txt Lactic acidosis. "Most Likely Diagnosis: -Congestive Heart Failure (CHF) with a comorbid complication of Cardiorenal Syndrome. - -Differential Diagnosis (from most to least probable): - -1. Cardiorenal Syndrome - Presence of heart failure, reduced ejection fraction, acute kidney injury, edema, and hypertension could be suggestive. -2. Chronic Kidney Disease (CKD) - Diabetes mellitus and hypertension could have damaged kidneys over time leading to edema, and acute kidney injury. -3. Sepsis secondary to Pneumonia - The pneumonia could have resulted in overwhelming infection leading to sepsis, could explain the fever, renal failure, and respiratory distress. -4. Decompensated heart failure - The congestive heart failure might have worsened leading to acute decompensation causing the edema, respiratory distress and reduced ejection fraction. -5. Chronic Obstructive Pulmonary Disease (COPD) exacerbation - The presence of obstructive sleep apnea could indicate underlying COPD, which in advanced stages could lead to heart failure, pulmonary hypertension and respiratory failure. -6. Thyrotoxicosis (Hyperthyroidism) - It could manifest as atrial fibrillation, heart failure, increased body weight and reduced ejection fraction. -7. Multiple System Atrophy (Shy-Drager syndrome) - This could cause various symptoms like falls, autonomic failure such as hypertension, sleep apnea, respiratory failure and early-onset hypertension. -8. Liver failure secondary to congestive hepatopathy - Symptoms like abdominal cramps, nausea, and edema might be related. -9. Ischemic Heart Disease - Left untreated can lead to heart failure, kidney injury, hypertension and atrial fibrillation. -10. Chronic pancreatitis - Diabetes mellitus, abdominal cramps, nausea, and obstructive sleep apnea could be an unusual manifestation. -11. Amyloidosis - Could be causing the heart failure, diabetes, atrial fibrillation, and kidney injury." -PMID_34818483-phenopacket-based_query.txt Cutaneous bacterial infection. "Given the mentioned symptom: - -Most likely diagnosis: Erythema multiforme - -Differential diagnosis, from most likely to least likely: - -1. Erythema multiforme -2. Erythema migrans (early Lyme disease) -3. Contact dermatitis -4. Allergic reaction -5. Psoriasis -6. Burn (thermal, chemical, or radiation-induced) -7. Cellulitis -8. Drug eruption -9. Photodermatitis -10. Rosacea -11. Erythema nodosum -12. Erythema toxicum neonatorum (rare in this age group)" -PMID_36260795-phenopacket-based_query.txt Drug reaction with eosinophilia and systemic symptoms complicated by eosinophilic myocarditis. "Most Likely Diagnosis: -Systemic Lupus Erythematosus (SLE) with a complication of Lupus Nephritis - -Differential Diagnosis Ranked by Probability: -1. Systemic Lupus Erythematosus (SLE) with Lupus Nephritis -2. Dermatomyositis -3. Hypothyroidism with heart failure -4. Acute renal failure due to Cardiorenal Syndrome -5. Polymyalgia Rheumatica -6. Addison's Disease -7. Metastatic cancer with paraneoplastic syndrome -8. Sarcoidosis -9. Congestive Heart Failure due to valve disease -10. Diabetes Mellitus with Diabetic Kidney Disease and Diabetic Myopathy -11. Severe malnutrition causing edema (kwashiorkor) -12. Chronic obstructive pulmonary disease (COPD) with pulmonary edema -13. Lymphoma with malignant infiltration of muscles. -14. Chronic Kidney Disease with related anemia and metabolite accumulation. -15. Hepatitis C with Cryoglobulinemia. -16. Dermatitis Herpetiformis with associated complications. -17. Severe liver disease leading to hypoalbuminemia and peripheral edema. -18. Amyloidosis -19. Adult Still’s Disease. -20. Vasculitis of the elderly (Giant Cell Arteritis). -" -PMID_36069875-phenopacket-based_query.txt Neuro-Behçet’s disease. "Most likely diagnosis: Behçet's Disease. - -Differential Diagnoses Ranked by Probability: - -1. Behçet's Disease: This condition is characterized by chronic inflammation leading to recurring symptoms such as oral and genital ulcers, and various eye-related issues like uveitis. The patient's symptoms match closely with several associated with Behçet's. - -2. Hughes-Stovin Syndrome: This is a very rare vasculitis disorder that can cause deep vein thrombosis, superior vena cava obstruction, pulmonary embolism, and aneurysms. - -3. Systemic Lupus Erythematosus (SLE): The symptoms of lupus can vary greatly, and involve many organ systems, including those presented here such as arthritis, headaches, and ulcers. - -4. Antiphospholipid Syndrome (APS): This is an autoimmune disorder characterized by excessive clotting, which can result in deep vein thrombosis, pulmonary emboli, and other related issues. - -5. Vasculitis such as Wegener's Granulomatosis: Generalized inflammation of the blood vessels can cause a diverse range of symptoms like those seen in this case. - -6. Neuro-Behçet's disease: This neurological variant of Behçet's presents mainly with neurologic symptoms, however, the systemic symptoms line up well with the patient presentation. - -7. Multiple Sclerosis (MS): MS usually manifests with neurologic symptoms. However, the diverse presentation can resemble the symptoms given here. - -8. Sarcoidosis: This is a multi-system disorder which can exhibit any of the given symptoms, albeit less likely than the ones listed above. - -9. Lyme Disease: dissemination of the Borrelia bacterium can lead to a variety of symptoms, depending on the organs affected. - -10. HIV/AIDS: The immune deficiency caused by this virus can lead to multiple systemic symptoms similar to those presented here due to various secondary infections or malignancies." -PMID_34965341-phenopacket-based_query.txt In summary, this patient’s history suggests that he had a transient ischemic attack, possibly due to moyamoya disease. To establish the diagnosis of moyamoya disease in this case, neuroimaging with angiography should be performed. "Most Likely Diagnosis: -Pediatric Multiple Sclerosis - -Differential Diagnosis: - -1. Pediatric Multiple Sclerosis -2. Guillain-Barre Syndrome -3. Lyme Disease -4. Acute Disseminated Encephalomyelitis -5. Neuroblastoma -6. Brain stem glioma -7. Hereditary Spastic Paraplegia -8. Leukemia with central nervous system involvement -9. Bell's Palsy -10. Metabolic or genetic disorders affecting the nervous system such as mitochondrial or lysosomal storage diseases" -PMID_34260840-phenopacket-based_query.txt another cause, listeria infection is the most likely diagnosis in this case. "Based on the provided information, my most likely diagnosis is Neurologic Lyme Disease. - -The robust differential diagnosis, ranked by their probability is as follows: - -1. Neurologic Lyme Disease -2. Tuberculous Meningitis -3. Enteroviral Meningitis -4. Systemic Lupus Erythematosus (lupus) -5. Neurosarcoidosis -6. Viral Encephalitis -7. Meningococcal Meningitis -8. Brucellosis -9. Rocky Mountain Spotted Fever -10. Bacterial Endocarditis." -PMID_33826823-phenopacket-based_query.txt Normal pressure hydrocephalus. "Most Likely Diagnosis: Normal Pressure Hydrocephalus - -Differential Diagnosis (ranked from most likely to least likely): -1. Normal Pressure Hydrocephalus -2. Cervical Myelopathy due to Spinal Canal Stenosis -3. Parkinson’s Disease (Parkinson's Plus Syndrome) -4. Multiple Sclerosis -5. Lewy Body Dementia -6. Cerebellar Ataxia -7. Alzheimer's Disease -8. Frontotemporal Dementia -9. Orthostatic Hypotension -10. Primary Progressive Multiple Sclerosis -11. Neurosyphilis -12. Binswanger's Disease -13. Multiple System Atrophy -14. Progressive Supranuclear Palsy -15. Wilson's Disease" From dbd1ce7fcaf0397a9cf4521db4dbc86fac38a4c4 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Thu, 18 Jul 2024 18:08:34 -0400 Subject: [PATCH 05/40] Move output parsers to utils dir --- output_parser.py => src/ontogpt/utils/output_parser.py | 0 .../ontogpt/utils/output_parser_bulleted.py | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename output_parser.py => src/ontogpt/utils/output_parser.py (100%) rename output_parser_bulleted.py => src/ontogpt/utils/output_parser_bulleted.py (100%) diff --git a/output_parser.py b/src/ontogpt/utils/output_parser.py similarity index 100% rename from output_parser.py rename to src/ontogpt/utils/output_parser.py diff --git a/output_parser_bulleted.py b/src/ontogpt/utils/output_parser_bulleted.py similarity index 100% rename from output_parser_bulleted.py rename to src/ontogpt/utils/output_parser_bulleted.py From 00eac34c09796db67ccb17afe456fadccf64d6f7 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Fri, 19 Jul 2024 10:46:47 -0400 Subject: [PATCH 06/40] Update docstrings for SoupClient --- src/ontogpt/clients/soup_client.py | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/src/ontogpt/clients/soup_client.py b/src/ontogpt/clients/soup_client.py index 8335b9f44..2863882e8 100644 --- a/src/ontogpt/clients/soup_client.py +++ b/src/ontogpt/clients/soup_client.py @@ -1,22 +1,19 @@ -"""Soup client.""" +"""BeautifulSoup client.""" from dataclasses import dataclass import requests from bs4 import BeautifulSoup -PMID = str - @dataclass class SoupClient: """A client for the Beautiful Soup API.""" def text(self, url: str) -> str: - """Get the text of a paper from its PMID. + """Get the text of a web site from its HTML. - :param id: - :param autoformat: if True include title and abstract concatenated + :param url: string containing the URL to extract text from :return: """ result = requests.get(url) From 42a0a2ad78b82386e5bfe981fd4daaf8f80d449b Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Fri, 19 Jul 2024 10:50:39 -0400 Subject: [PATCH 07/40] Update docstrings for WikipediaClient --- src/ontogpt/clients/wikipedia_client.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontogpt/clients/wikipedia_client.py b/src/ontogpt/clients/wikipedia_client.py index a96bb0c04..c023bb62c 100644 --- a/src/ontogpt/clients/wikipedia_client.py +++ b/src/ontogpt/clients/wikipedia_client.py @@ -1,4 +1,4 @@ -"""Pubmed Client.""" +"""Wikipedia Client.""" from dataclasses import dataclass @@ -8,12 +8,12 @@ @dataclass class WikipediaClient: - """A client for Wikipedia articles.""" + """A client for extracting text from Wikipedia articles.""" language: str = "en" def text(self, title: str) -> str: - """Get the text of a an article.""" + """Get the text of an article.""" wiki = wikipediaapi.Wikipedia("ontogpt", self.language) page = wiki.page(title) From 947e03ec147c0441c560f4da4d43888120e4b877 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Fri, 19 Jul 2024 10:51:31 -0400 Subject: [PATCH 08/40] Linting/formatting in engines --- src/ontogpt/engines/embedding_similarity_engine.py | 1 + src/ontogpt/engines/resolver.py | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/src/ontogpt/engines/embedding_similarity_engine.py b/src/ontogpt/engines/embedding_similarity_engine.py index 79b7bd326..09ca5a8e1 100644 --- a/src/ontogpt/engines/embedding_similarity_engine.py +++ b/src/ontogpt/engines/embedding_similarity_engine.py @@ -1,4 +1,5 @@ """Similarity engine.""" + import logging from dataclasses import dataclass from typing import Iterable, List diff --git a/src/ontogpt/engines/resolver.py b/src/ontogpt/engines/resolver.py index 94543bb99..9b016458a 100644 --- a/src/ontogpt/engines/resolver.py +++ b/src/ontogpt/engines/resolver.py @@ -1,4 +1,5 @@ """Resolver engine.""" + from typing import Optional, Type, Union from class_resolver import ClassResolver @@ -21,6 +22,6 @@ def create_engine( if isinstance(engine, str): engine = resolver.get_class(engine)(**kwargs) if engine is not None and not isinstance(engine, str): - return engine(template_details=template_details, **kwargs) # type: ignore + return engine(template_details=template_details, **kwargs) # type: ignore else: return SPIRESEngine # type: ignore From b22dd9355694c100f648e17ff6d034394f86472c Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Fri, 19 Jul 2024 10:53:36 -0400 Subject: [PATCH 09/40] Remove projects dir - this isn't contributing much --- .../biological_process/biological_process.py | 558 ----- .../docs/AnnotatorResult.md | 22 - projects/biological_process/docs/Any.md | 25 - .../docs/BiologicalProcess.md | 56 - .../biological_process/docs/ChemicalEntity.md | 35 - .../docs/CompoundExpression.md | 20 - .../docs/ExtractionResult.md | 32 - projects/biological_process/docs/Gene.md | 35 - .../docs/GeneMolecularActivityRelationship.md | 24 - .../docs/MolecularActivity.md | 35 - .../biological_process/docs/NamedEntity.md | 37 - 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652994ad1..000000000 --- a/projects/biological_process/biological_process.py +++ /dev/null @@ -1,558 +0,0 @@ -# Auto generated from biological_process.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:51:21 -# Schema: biological-process-template -# -# id: https://w3id.org/ontogpt/biological_process -# description: A template for GO-CAMs -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CHEBI = CurieNamespace('CHEBI', 'http://example.org/UNKNOWN/CHEBI/') -GO = CurieNamespace('GO', 'http://example.org/UNKNOWN/GO/') -HGNC = CurieNamespace('HGNC', 'http://example.org/UNKNOWN/HGNC/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -BP = CurieNamespace('bp', 'http://w3id.org/ontogpt/biological-process-template') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = BP - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class BiologicalProcessId(NamedEntityId): - pass - - -class GeneId(NamedEntityId): - pass - - -class MolecularActivityId(NamedEntityId): - pass - - -class ChemicalEntityId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class GeneMolecularActivityRelationship(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.GeneMolecularActivityRelationship - class_class_curie: ClassVar[str] = "bp:GeneMolecularActivityRelationship" - class_name: ClassVar[str] = "GeneMolecularActivityRelationship" - class_model_uri: ClassVar[URIRef] = BP.GeneMolecularActivityRelationship - - gene: Optional[Union[str, GeneId]] = None - molecular_activity: Optional[Union[str, MolecularActivityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.molecular_activity is not None and not isinstance(self.molecular_activity, MolecularActivityId): - self.molecular_activity = MolecularActivityId(self.molecular_activity) - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = BP.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = BP.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class BiologicalProcess(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.BiologicalProcess - class_class_curie: ClassVar[str] = "bp:BiologicalProcess" - class_name: ClassVar[str] = "BiologicalProcess" - class_model_uri: ClassVar[URIRef] = BP.BiologicalProcess - - id: Union[str, BiologicalProcessId] = None - label: Optional[str] = None - description: Optional[str] = None - synonyms: Optional[Union[str, List[str]]] = empty_list() - subclass_of: Optional[Union[str, BiologicalProcessId]] = None - inputs: Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]] = empty_list() - outputs: Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]] = empty_list() - steps: Optional[Union[Union[str, MolecularActivityId], List[Union[str, MolecularActivityId]]]] = empty_list() - genes: Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]] = empty_list() - gene_activities: Optional[Union[Union[dict, "GeneMolecularActivityRelationship"], List[Union[dict, "GeneMolecularActivityRelationship"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, BiologicalProcessId): - self.id = BiologicalProcessId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.synonyms, list): - self.synonyms = [self.synonyms] if self.synonyms is not None else [] - self.synonyms = [v if isinstance(v, str) else str(v) for v in self.synonyms] - - if self.subclass_of is not None and not isinstance(self.subclass_of, BiologicalProcessId): - self.subclass_of = BiologicalProcessId(self.subclass_of) - - if not isinstance(self.inputs, list): - self.inputs = [self.inputs] if self.inputs is not None else [] - self.inputs = [v if isinstance(v, ChemicalEntityId) else ChemicalEntityId(v) for v in self.inputs] - - if not isinstance(self.outputs, list): - self.outputs = [self.outputs] if self.outputs is not None else [] - self.outputs = [v if isinstance(v, ChemicalEntityId) else ChemicalEntityId(v) for v in self.outputs] - - if not isinstance(self.steps, list): - self.steps = [self.steps] if self.steps is not None else [] - self.steps = [v if isinstance(v, MolecularActivityId) else MolecularActivityId(v) for v in self.steps] - - if not isinstance(self.genes, list): - self.genes = [self.genes] if self.genes is not None else [] - self.genes = [v if isinstance(v, GeneId) else GeneId(v) for v in self.genes] - - if not isinstance(self.gene_activities, list): - self.gene_activities = [self.gene_activities] if self.gene_activities is not None else [] - self.gene_activities = [v if isinstance(v, GeneMolecularActivityRelationship) else GeneMolecularActivityRelationship(**as_dict(v)) for v in self.gene_activities] - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.Gene - class_class_curie: ClassVar[str] = "bp:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = BP.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class MolecularActivity(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.MolecularActivity - class_class_curie: ClassVar[str] = "bp:MolecularActivity" - class_name: ClassVar[str] = "MolecularActivity" - class_model_uri: ClassVar[URIRef] = BP.MolecularActivity - - id: Union[str, MolecularActivityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MolecularActivityId): - self.id = MolecularActivityId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalEntity(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.ChemicalEntity - class_class_curie: ClassVar[str] = "bp:ChemicalEntity" - class_name: ClassVar[str] = "ChemicalEntity" - class_model_uri: ClassVar[URIRef] = BP.ChemicalEntity - - id: Union[str, ChemicalEntityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalEntityId): - self.id = ChemicalEntityId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = BP.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = BP.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = BP.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = BP.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = BP.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = BP.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.biologicalProcess__label = Slot(uri=BP.label, name="biologicalProcess__label", curie=BP.curie('label'), - model_uri=BP.biologicalProcess__label, domain=None, range=Optional[str]) - -slots.biologicalProcess__description = Slot(uri=BP.description, name="biologicalProcess__description", curie=BP.curie('description'), - model_uri=BP.biologicalProcess__description, domain=None, range=Optional[str]) - -slots.biologicalProcess__synonyms = Slot(uri=BP.synonyms, name="biologicalProcess__synonyms", curie=BP.curie('synonyms'), - model_uri=BP.biologicalProcess__synonyms, domain=None, range=Optional[Union[str, List[str]]]) - -slots.biologicalProcess__subclass_of = Slot(uri=BP.subclass_of, name="biologicalProcess__subclass_of", curie=BP.curie('subclass_of'), - model_uri=BP.biologicalProcess__subclass_of, domain=None, range=Optional[Union[str, BiologicalProcessId]]) - -slots.biologicalProcess__inputs = Slot(uri=BP.inputs, name="biologicalProcess__inputs", curie=BP.curie('inputs'), - model_uri=BP.biologicalProcess__inputs, domain=None, range=Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]]) - -slots.biologicalProcess__outputs = Slot(uri=BP.outputs, name="biologicalProcess__outputs", curie=BP.curie('outputs'), - model_uri=BP.biologicalProcess__outputs, domain=None, range=Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]]) - -slots.biologicalProcess__steps = Slot(uri=BP.steps, name="biologicalProcess__steps", curie=BP.curie('steps'), - model_uri=BP.biologicalProcess__steps, domain=None, range=Optional[Union[Union[str, MolecularActivityId], List[Union[str, MolecularActivityId]]]]) - -slots.biologicalProcess__genes = Slot(uri=BP.genes, name="biologicalProcess__genes", curie=BP.curie('genes'), - model_uri=BP.biologicalProcess__genes, domain=None, range=Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]]) - -slots.biologicalProcess__gene_activities = Slot(uri=BP.gene_activities, name="biologicalProcess__gene_activities", curie=BP.curie('gene_activities'), - model_uri=BP.biologicalProcess__gene_activities, domain=None, range=Optional[Union[Union[dict, GeneMolecularActivityRelationship], List[Union[dict, GeneMolecularActivityRelationship]]]]) - -slots.geneMolecularActivityRelationship__gene = Slot(uri=BP.gene, name="geneMolecularActivityRelationship__gene", curie=BP.curie('gene'), - model_uri=BP.geneMolecularActivityRelationship__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneMolecularActivityRelationship__molecular_activity = Slot(uri=BP.molecular_activity, name="geneMolecularActivityRelationship__molecular_activity", curie=BP.curie('molecular_activity'), - model_uri=BP.geneMolecularActivityRelationship__molecular_activity, domain=None, range=Optional[Union[str, MolecularActivityId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=BP.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=BP.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=BP.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=BP.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=BP.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=BP.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=BP.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=BP.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=BP.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=BP.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=BP.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=BP.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=BP.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=BP.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=BP.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=BP.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=BP.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=BP.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=BP.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=BP.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=BP.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=BP.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=BP.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=BP.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=BP.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/biological_process/docs/AnnotatorResult.md b/projects/biological_process/docs/AnnotatorResult.md deleted file mode 100644 index b25d0a529..000000000 --- a/projects/biological_process/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [bp:AnnotatorResult](http://w3id.org/ontogpt/biological-process-templateAnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) 0..1 - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) 0..1 - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) 0..1 - * Range: [String](types/String.md) diff --git a/projects/biological_process/docs/Any.md b/projects/biological_process/docs/Any.md deleted file mode 100644 index cb46c4be4..000000000 --- a/projects/biological_process/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [bp:Any](http://w3id.org/ontogpt/biological-process-templateAny) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* 0..1 **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* 0..\* **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/biological_process/docs/BiologicalProcess.md b/projects/biological_process/docs/BiologicalProcess.md deleted file mode 100644 index 777220560..000000000 --- a/projects/biological_process/docs/BiologicalProcess.md +++ /dev/null @@ -1,56 +0,0 @@ - -# Class: BiologicalProcess - - - - -URI: [bp:BiologicalProcess](http://w3id.org/ontogpt/biological-process-templateBiologicalProcess) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MolecularActivity],[GeneMolecularActivityRelationship],[Gene],[ChemicalEntity],[GeneMolecularActivityRelationship]0..1 **[BiologicalProcess](BiologicalProcess.md)** - -## Attributes - - -### Own - - * [➞label](biologicalProcess__label.md) 0..1 - * Description: the name of the biological process - * Range: [String](types/String.md) - * [➞description](biologicalProcess__description.md) 0..1 - * Description: a textual description of the biological process - * Range: [String](types/String.md) - * [➞synonyms](biologicalProcess__synonyms.md) 0..\* - * Description: alternative names of the biological process - * Range: [String](types/String.md) - * [➞subclass_of](biologicalProcess__subclass_of.md) 0..1 - * Description: the category to which this biological process belongs - * Range: [BiologicalProcess](BiologicalProcess.md) - * [➞inputs](biologicalProcess__inputs.md) 0..\* - * Description: the inputs of the biological process - * Range: [ChemicalEntity](ChemicalEntity.md) - * [➞outputs](biologicalProcess__outputs.md) 0..\* - * Description: the outputs of the biological process - * Range: [ChemicalEntity](ChemicalEntity.md) - * [➞steps](biologicalProcess__steps.md) 0..\* - * Description: the steps involved in this biological process - * Range: [MolecularActivity](MolecularActivity.md) - * [➞genes](biologicalProcess__genes.md) 0..\* - * Range: [Gene](Gene.md) - * [➞gene_activities](biologicalProcess__gene_activities.md) 0..\* - * Description: semicolon-separated list of gene to molecular activity relationships - * Range: [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) diff --git a/projects/biological_process/docs/ChemicalEntity.md b/projects/biological_process/docs/ChemicalEntity.md deleted file mode 100644 index 8d1b59df9..000000000 --- a/projects/biological_process/docs/ChemicalEntity.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: ChemicalEntity - - - - -URI: [bp:ChemicalEntity](http://w3id.org/ontogpt/biological-process-templateChemicalEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20inputs%200..*>[ChemicalEntity|id(i):string;label(i):string%20%3F],[BiologicalProcess]-%20outputs%200..*>[ChemicalEntity],[NamedEntity]^-[ChemicalEntity],[BiologicalProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20inputs%200..*>[ChemicalEntity|id(i):string;label(i):string%20%3F],[BiologicalProcess]-%20outputs%200..*>[ChemicalEntity],[NamedEntity]^-[ChemicalEntity],[BiologicalProcess]) - -## Identifier prefixes - - * CHEBI - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞inputs](biologicalProcess__inputs.md)* 0..\* **[ChemicalEntity](ChemicalEntity.md)** - * **None** *[➞outputs](biologicalProcess__outputs.md)* 0..\* **[ChemicalEntity](ChemicalEntity.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biological_process/docs/CompoundExpression.md b/projects/biological_process/docs/CompoundExpression.md deleted file mode 100644 index 6c1bba32f..000000000 --- a/projects/biological_process/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [bp:CompoundExpression](http://w3id.org/ontogpt/biological-process-templateCompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/biological_process/docs/ExtractionResult.md b/projects/biological_process/docs/ExtractionResult.md deleted file mode 100644 index 4d0ab7ab9..000000000 --- a/projects/biological_process/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [bp:ExtractionResult](http://w3id.org/ontogpt/biological-process-templateExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]0..1 - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) 0..1 - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) 0..1 - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) 0..1 - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) 0..1 - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) 0..1 - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) 0..\* - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/biological_process/docs/Gene.md b/projects/biological_process/docs/Gene.md deleted file mode 100644 index ec2822f49..000000000 --- a/projects/biological_process/docs/Gene.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Gene - - - - -URI: [bp:Gene](http://w3id.org/ontogpt/biological-process-templateGene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20genes%200..*>[Gene|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20gene%200..1>[Gene],[NamedEntity]^-[Gene],[GeneMolecularActivityRelationship],[BiologicalProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20genes%200..*>[Gene|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20gene%200..1>[Gene],[NamedEntity]^-[Gene],[GeneMolecularActivityRelationship],[BiologicalProcess]) - -## Identifier prefixes - - * HGNC - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞genes](biologicalProcess__genes.md)* 0..\* **[Gene](Gene.md)** - * **None** *[➞gene](geneMolecularActivityRelationship__gene.md)* 0..1 **[Gene](Gene.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biological_process/docs/GeneMolecularActivityRelationship.md b/projects/biological_process/docs/GeneMolecularActivityRelationship.md deleted file mode 100644 index d85f3d3cf..000000000 --- a/projects/biological_process/docs/GeneMolecularActivityRelationship.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Class: GeneMolecularActivityRelationship - - - - -URI: [bp:GeneMolecularActivityRelationship](http://w3id.org/ontogpt/biological-process-templateGeneMolecularActivityRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[MolecularActivity],[MolecularActivity][GeneMolecularActivityRelationship],[Gene],[BiologicalProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[MolecularActivity],[MolecularActivity][GeneMolecularActivityRelationship],[Gene],[BiologicalProcess]) - -## Referenced by Class - - * **None** *[➞gene_activities](biologicalProcess__gene_activities.md)* 0..\* **[GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md)** - -## Attributes - - -### Own - - * [➞gene](geneMolecularActivityRelationship__gene.md) 0..1 - * Range: [Gene](Gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md) 0..1 - * Range: [MolecularActivity](MolecularActivity.md) diff --git a/projects/biological_process/docs/MolecularActivity.md b/projects/biological_process/docs/MolecularActivity.md deleted file mode 100644 index d3f34ec4f..000000000 --- a/projects/biological_process/docs/MolecularActivity.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: MolecularActivity - - - - -URI: [bp:MolecularActivity](http://w3id.org/ontogpt/biological-process-templateMolecularActivity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20steps%200..*>[MolecularActivity|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20molecular_activity%200..1>[MolecularActivity],[NamedEntity]^-[MolecularActivity],[GeneMolecularActivityRelationship],[BiologicalProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BiologicalProcess]-%20steps%200..*>[MolecularActivity|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20molecular_activity%200..1>[MolecularActivity],[NamedEntity]^-[MolecularActivity],[GeneMolecularActivityRelationship],[BiologicalProcess]) - -## Identifier prefixes - - * GO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞steps](biologicalProcess__steps.md)* 0..\* **[MolecularActivity](MolecularActivity.md)** - * **None** *[➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md)* 0..1 **[MolecularActivity](MolecularActivity.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biological_process/docs/NamedEntity.md b/projects/biological_process/docs/NamedEntity.md deleted file mode 100644 index db2c7c939..000000000 --- a/projects/biological_process/docs/NamedEntity.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [bp:NamedEntity](http://w3id.org/ontogpt/biological-process-templateNamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[MolecularActivity],[NamedEntity]^-[Gene],[NamedEntity]^-[ChemicalEntity],[NamedEntity]^-[BiologicalProcess],[Triple],[MolecularActivity],[Gene],[ChemicalEntity],[BiologicalProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[MolecularActivity],[NamedEntity]^-[Gene],[NamedEntity]^-[ChemicalEntity],[NamedEntity]^-[BiologicalProcess],[Triple],[MolecularActivity],[Gene],[ChemicalEntity],[BiologicalProcess]) - -## Children - - * [BiologicalProcess](BiologicalProcess.md) - * [ChemicalEntity](ChemicalEntity.md) - * [Gene](Gene.md) - * [MolecularActivity](MolecularActivity.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* 0..1 **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biological_process/docs/NullDataOptions.md b/projects/biological_process/docs/NullDataOptions.md deleted file mode 100644 index 716244681..000000000 --- a/projects/biological_process/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [bp:NullDataOptions](http://w3id.org/ontogpt/biological-process-templateNullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/biological_process/docs/Publication.md b/projects/biological_process/docs/Publication.md deleted file mode 100644 index d54b928f4..000000000 --- a/projects/biological_process/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [bp:Publication](http://w3id.org/ontogpt/biological-process-templatePublication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* 0..1 **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) 0..1 - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) 0..1 - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) 0..1 - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) 0..1 - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) 0..1 - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/biological_process/docs/RelationshipType.md b/projects/biological_process/docs/RelationshipType.md deleted file mode 100644 index 918e3647c..000000000 --- a/projects/biological_process/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [bp:RelationshipType](http://w3id.org/ontogpt/biological-process-templateRelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* 0..1 **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biological_process/docs/TextWithTriples.md b/projects/biological_process/docs/TextWithTriples.md deleted file mode 100644 index 4237a7785..000000000 --- a/projects/biological_process/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [bp:TextWithTriples](http://w3id.org/ontogpt/biological-process-templateTextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]0..1 - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) 0..\* - * Range: [Triple](Triple.md) diff --git a/projects/biological_process/docs/Triple.md b/projects/biological_process/docs/Triple.md deleted file mode 100644 index b9e6bb42d..000000000 --- a/projects/biological_process/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [bp:Triple](http://w3id.org/ontogpt/biological-process-templateTriple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity][Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity][Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* 0..\* **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) 0..1 - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) 0..1 - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) 0..1 - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) 0..1 - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) 0..1 - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) 0..1 - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/biological_process/docs/annotatorResult__object_id.md b/projects/biological_process/docs/annotatorResult__object_id.md deleted file mode 100644 index ffc6bbeca..000000000 --- a/projects/biological_process/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [bp:annotatorResult__object_id](http://w3id.org/ontogpt/biological-process-templateannotatorResult__object_id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/biological_process/docs/annotatorResult__object_text.md b/projects/biological_process/docs/annotatorResult__object_text.md deleted file mode 100644 index b127369af..000000000 --- a/projects/biological_process/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [bp:annotatorResult__object_text](http://w3id.org/ontogpt/biological-process-templateannotatorResult__object_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/biological_process/docs/annotatorResult__subject_text.md b/projects/biological_process/docs/annotatorResult__subject_text.md deleted file mode 100644 index 79e732b09..000000000 --- a/projects/biological_process/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [bp:annotatorResult__subject_text](http://w3id.org/ontogpt/biological-process-templateannotatorResult__subject_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/biological_process/docs/biologicalProcess__description.md b/projects/biological_process/docs/biologicalProcess__description.md deleted file mode 100644 index dfe2423fe..000000000 --- a/projects/biological_process/docs/biologicalProcess__description.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: description - - -a textual description of the biological process - -URI: [bp:biologicalProcess__description](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__description) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biologicalProcess__gene_activities.md b/projects/biological_process/docs/biologicalProcess__gene_activities.md deleted file mode 100644 index 19ca2e4a1..000000000 --- a/projects/biological_process/docs/biologicalProcess__gene_activities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_activities - - -semicolon-separated list of gene to molecular activity relationships - -URI: [bp:biologicalProcess__gene_activities](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__gene_activities) - - -## Domain and Range - -None → 0..\* [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biologicalProcess__genes.md b/projects/biological_process/docs/biologicalProcess__genes.md deleted file mode 100644 index f4db39472..000000000 --- a/projects/biological_process/docs/biologicalProcess__genes.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: genes - - - - -URI: [bp:biologicalProcess__genes](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__genes) - - -## Domain and Range - -None → 0..\* [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biologicalProcess__inputs.md b/projects/biological_process/docs/biologicalProcess__inputs.md deleted file mode 100644 index b847140f1..000000000 --- a/projects/biological_process/docs/biologicalProcess__inputs.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: inputs - - -the inputs of the biological process - -URI: [bp:biologicalProcess__inputs](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__inputs) - - -## Domain and Range - -None → 0..\* [ChemicalEntity](ChemicalEntity.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biologicalProcess__label.md b/projects/biological_process/docs/biologicalProcess__label.md deleted file mode 100644 index dbfb32e50..000000000 --- a/projects/biological_process/docs/biologicalProcess__label.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: label - - -the name of the biological process - -URI: [bp:biologicalProcess__label](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__label) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biologicalProcess__outputs.md b/projects/biological_process/docs/biologicalProcess__outputs.md deleted file mode 100644 index 06b35c922..000000000 --- a/projects/biological_process/docs/biologicalProcess__outputs.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: outputs - - -the outputs of the biological process - -URI: [bp:biologicalProcess__outputs](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__outputs) - - -## Domain and Range - -None → 0..\* [ChemicalEntity](ChemicalEntity.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biologicalProcess__steps.md b/projects/biological_process/docs/biologicalProcess__steps.md deleted file mode 100644 index d7a2bf166..000000000 --- a/projects/biological_process/docs/biologicalProcess__steps.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: steps - - -the steps involved in this biological process - -URI: [bp:biologicalProcess__steps](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__steps) - - -## Domain and Range - -None → 0..\* [MolecularActivity](MolecularActivity.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biologicalProcess__subclass_of.md b/projects/biological_process/docs/biologicalProcess__subclass_of.md deleted file mode 100644 index 1356361a6..000000000 --- a/projects/biological_process/docs/biologicalProcess__subclass_of.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subclass_of - - -the category to which this biological process belongs - -URI: [bp:biologicalProcess__subclass_of](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__subclass_of) - - -## Domain and Range - -None → 0..1 [BiologicalProcess](BiologicalProcess.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biologicalProcess__synonyms.md b/projects/biological_process/docs/biologicalProcess__synonyms.md deleted file mode 100644 index 5a7ea0d18..000000000 --- a/projects/biological_process/docs/biologicalProcess__synonyms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: synonyms - - -alternative names of the biological process - -URI: [bp:biologicalProcess__synonyms](http://w3id.org/ontogpt/biological-process-templatebiologicalProcess__synonyms) - - -## Domain and Range - -None → 0..\* [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) diff --git a/projects/biological_process/docs/biological_process.md b/projects/biological_process/docs/biological_process.md deleted file mode 100644 index effdf9cb9..000000000 --- a/projects/biological_process/docs/biological_process.md +++ /dev/null @@ -1,119 +0,0 @@ - -# biological-process-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for GO-CAMs - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - * [NamedEntity](NamedEntity.md) - * [BiologicalProcess](BiologicalProcess.md) - * [ChemicalEntity](ChemicalEntity.md) - * [Gene](Gene.md) - * [MolecularActivity](MolecularActivity.md) - * [RelationshipType](RelationshipType.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞description](biologicalProcess__description.md) - a textual description of the biological process - * [➞gene_activities](biologicalProcess__gene_activities.md) - semicolon-separated list of gene to molecular activity relationships - * [➞genes](biologicalProcess__genes.md) - * [➞inputs](biologicalProcess__inputs.md) - the inputs of the biological process - * [➞label](biologicalProcess__label.md) - the name of the biological process - * [➞outputs](biologicalProcess__outputs.md) - the outputs of the biological process - * [➞steps](biologicalProcess__steps.md) - the steps involved in this biological process - * [➞subclass_of](biologicalProcess__subclass_of.md) - the category to which this biological process belongs - * [➞synonyms](biologicalProcess__synonyms.md) - alternative names of the biological process - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞gene](geneMolecularActivityRelationship__gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/biological_process/docs/extractionResult__extracted_object.md b/projects/biological_process/docs/extractionResult__extracted_object.md deleted file mode 100644 index 9cb7fab08..000000000 --- a/projects/biological_process/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [bp:extractionResult__extracted_object](http://w3id.org/ontogpt/biological-process-templateextractionResult__extracted_object) - - -## Domain and Range - -None → 0..1 [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biological_process/docs/extractionResult__input_id.md b/projects/biological_process/docs/extractionResult__input_id.md deleted file mode 100644 index 77a58c462..000000000 --- a/projects/biological_process/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [bp:extractionResult__input_id](http://w3id.org/ontogpt/biological-process-templateextractionResult__input_id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biological_process/docs/extractionResult__input_text.md b/projects/biological_process/docs/extractionResult__input_text.md deleted file mode 100644 index 0d447a742..000000000 --- a/projects/biological_process/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [bp:extractionResult__input_text](http://w3id.org/ontogpt/biological-process-templateextractionResult__input_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biological_process/docs/extractionResult__input_title.md b/projects/biological_process/docs/extractionResult__input_title.md deleted file mode 100644 index 87d22e4d5..000000000 --- a/projects/biological_process/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [bp:extractionResult__input_title](http://w3id.org/ontogpt/biological-process-templateextractionResult__input_title) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biological_process/docs/extractionResult__named_entities.md b/projects/biological_process/docs/extractionResult__named_entities.md deleted file mode 100644 index 4274e9c2a..000000000 --- a/projects/biological_process/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [bp:extractionResult__named_entities](http://w3id.org/ontogpt/biological-process-templateextractionResult__named_entities) - - -## Domain and Range - -None → 0..\* [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biological_process/docs/extractionResult__prompt.md b/projects/biological_process/docs/extractionResult__prompt.md deleted file mode 100644 index 2d9f03d71..000000000 --- a/projects/biological_process/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [bp:extractionResult__prompt](http://w3id.org/ontogpt/biological-process-templateextractionResult__prompt) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biological_process/docs/extractionResult__raw_completion_output.md b/projects/biological_process/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 0e689fc73..000000000 --- a/projects/biological_process/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [bp:extractionResult__raw_completion_output](http://w3id.org/ontogpt/biological-process-templateextractionResult__raw_completion_output) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biological_process/docs/geneMolecularActivityRelationship__gene.md b/projects/biological_process/docs/geneMolecularActivityRelationship__gene.md deleted file mode 100644 index 3f0e4bbab..000000000 --- a/projects/biological_process/docs/geneMolecularActivityRelationship__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [bp:geneMolecularActivityRelationship__gene](http://w3id.org/ontogpt/biological-process-templategeneMolecularActivityRelationship__gene) - - -## Domain and Range - -None → 0..1 [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) diff --git a/projects/biological_process/docs/geneMolecularActivityRelationship__molecular_activity.md b/projects/biological_process/docs/geneMolecularActivityRelationship__molecular_activity.md deleted file mode 100644 index 6fe3e9323..000000000 --- a/projects/biological_process/docs/geneMolecularActivityRelationship__molecular_activity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: molecular_activity - - - - -URI: [bp:geneMolecularActivityRelationship__molecular_activity](http://w3id.org/ontogpt/biological-process-templategeneMolecularActivityRelationship__molecular_activity) - - -## Domain and Range - -None → 0..1 [MolecularActivity](MolecularActivity.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) diff --git a/projects/biological_process/docs/namedEntity__id.md b/projects/biological_process/docs/namedEntity__id.md deleted file mode 100644 index df74e8512..000000000 --- a/projects/biological_process/docs/namedEntity__id.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [bp:namedEntity__id](http://w3id.org/ontogpt/biological-process-templatenamedEntity__id) - - -## Domain and Range - -None → 1..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [BiologicalProcess](BiologicalProcess.md) - * [ChemicalEntity](ChemicalEntity.md) - * [Gene](Gene.md) - * [MolecularActivity](MolecularActivity.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/biological_process/docs/namedEntity__label.md b/projects/biological_process/docs/namedEntity__label.md deleted file mode 100644 index 5db5381b4..000000000 --- a/projects/biological_process/docs/namedEntity__label.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [bp:namedEntity__label](http://w3id.org/ontogpt/biological-process-templatenamedEntity__label) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ChemicalEntity](ChemicalEntity.md) - * [Gene](Gene.md) - * [MolecularActivity](MolecularActivity.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/biological_process/docs/publication__abstract.md b/projects/biological_process/docs/publication__abstract.md deleted file mode 100644 index 96be47057..000000000 --- a/projects/biological_process/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [bp:publication__abstract](http://w3id.org/ontogpt/biological-process-templatepublication__abstract) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biological_process/docs/publication__combined_text.md b/projects/biological_process/docs/publication__combined_text.md deleted file mode 100644 index 613506acc..000000000 --- a/projects/biological_process/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [bp:publication__combined_text](http://w3id.org/ontogpt/biological-process-templatepublication__combined_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biological_process/docs/publication__full_text.md b/projects/biological_process/docs/publication__full_text.md deleted file mode 100644 index 978e83538..000000000 --- a/projects/biological_process/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [bp:publication__full_text](http://w3id.org/ontogpt/biological-process-templatepublication__full_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biological_process/docs/publication__id.md b/projects/biological_process/docs/publication__id.md deleted file mode 100644 index 9c03571b0..000000000 --- a/projects/biological_process/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [bp:publication__id](http://w3id.org/ontogpt/biological-process-templatepublication__id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biological_process/docs/publication__title.md b/projects/biological_process/docs/publication__title.md deleted file mode 100644 index 93aa90543..000000000 --- a/projects/biological_process/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [bp:publication__title](http://w3id.org/ontogpt/biological-process-templatepublication__title) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biological_process/docs/textWithTriples__publication.md b/projects/biological_process/docs/textWithTriples__publication.md deleted file mode 100644 index d5eb7b7f9..000000000 --- a/projects/biological_process/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [bp:textWithTriples__publication](http://w3id.org/ontogpt/biological-process-templatetextWithTriples__publication) - - -## Domain and Range - -None → 0..1 [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/biological_process/docs/textWithTriples__triples.md b/projects/biological_process/docs/textWithTriples__triples.md deleted file mode 100644 index 4865a084d..000000000 --- a/projects/biological_process/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [bp:textWithTriples__triples](http://w3id.org/ontogpt/biological-process-templatetextWithTriples__triples) - - -## Domain and Range - -None → 0..\* [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/biological_process/docs/triple__object.md b/projects/biological_process/docs/triple__object.md deleted file mode 100644 index bc102f3c8..000000000 --- a/projects/biological_process/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [bp:triple__object](http://w3id.org/ontogpt/biological-process-templatetriple__object) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biological_process/docs/triple__object_qualifier.md b/projects/biological_process/docs/triple__object_qualifier.md deleted file mode 100644 index f06d74b8d..000000000 --- a/projects/biological_process/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [bp:triple__object_qualifier](http://w3id.org/ontogpt/biological-process-templatetriple__object_qualifier) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biological_process/docs/triple__predicate.md b/projects/biological_process/docs/triple__predicate.md deleted file mode 100644 index 92c257664..000000000 --- a/projects/biological_process/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [bp:triple__predicate](http://w3id.org/ontogpt/biological-process-templatetriple__predicate) - - -## Domain and Range - -None → 0..1 [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biological_process/docs/triple__qualifier.md b/projects/biological_process/docs/triple__qualifier.md deleted file mode 100644 index 1ea0152f1..000000000 --- a/projects/biological_process/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [bp:triple__qualifier](http://w3id.org/ontogpt/biological-process-templatetriple__qualifier) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biological_process/docs/triple__subject.md b/projects/biological_process/docs/triple__subject.md deleted file mode 100644 index cc0377542..000000000 --- a/projects/biological_process/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [bp:triple__subject](http://w3id.org/ontogpt/biological-process-templatetriple__subject) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biological_process/docs/triple__subject_qualifier.md b/projects/biological_process/docs/triple__subject_qualifier.md deleted file mode 100644 index 998e0615e..000000000 --- a/projects/biological_process/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [bp:triple__subject_qualifier](http://w3id.org/ontogpt/biological-process-templatetriple__subject_qualifier) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biological_process/docs/types/Boolean.md b/projects/biological_process/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/biological_process/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/biological_process/docs/types/Curie.md b/projects/biological_process/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/biological_process/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/biological_process/docs/types/Date.md b/projects/biological_process/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/biological_process/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/biological_process/docs/types/DateOrDatetime.md b/projects/biological_process/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/biological_process/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/biological_process/docs/types/Datetime.md b/projects/biological_process/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/biological_process/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/biological_process/docs/types/Decimal.md b/projects/biological_process/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/biological_process/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/biological_process/docs/types/Double.md b/projects/biological_process/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/biological_process/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/biological_process/docs/types/Float.md b/projects/biological_process/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/biological_process/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/biological_process/docs/types/Integer.md b/projects/biological_process/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/biological_process/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/biological_process/docs/types/Jsonpath.md b/projects/biological_process/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/biological_process/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/biological_process/docs/types/Jsonpointer.md b/projects/biological_process/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/biological_process/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/biological_process/docs/types/Ncname.md b/projects/biological_process/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/biological_process/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/biological_process/docs/types/Nodeidentifier.md b/projects/biological_process/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/biological_process/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/biological_process/docs/types/Objectidentifier.md b/projects/biological_process/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/biological_process/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/biological_process/docs/types/Sparqlpath.md b/projects/biological_process/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/biological_process/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/biological_process/docs/types/String.md b/projects/biological_process/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/biological_process/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/biological_process/docs/types/Time.md b/projects/biological_process/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/biological_process/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/biological_process/docs/types/Uri.md b/projects/biological_process/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/biological_process/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range 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zXhkLE397JxqHlB}4{AJF9HKZzOF+)i7mYrOpkr%JbpHydc;Gf z`!RHx_oNddC6XsByLgBfQHbPQOBY#m&Z|Y@%5jFwTZ-hlo0ay0WY`ePy2c)TfZK$? zcn>EAv3m4nZA52}EIB_V=u>!Sk1jd?0ogGVez(!Ofc%8xrkba_S@Tp*TlZlb z=?XI75Ll3Zf9e6G_Q#hO$PWMY48&9Er)LoUk_7|v0x$b#>Hj>D@KpTiCjBq*A<*Cd zVaxt0z|&2de*k!+!aV}~am(f@%F|Zu7s>?46G6*(it@N;@UNrDf{NT9P#y>1|2j%H z(jQSCr@2p2o(>~_J&^#)A5k7hlTT5e&eMLOw1cYIAD-xOy7m<1=`iUR3L@y(${$c3 zM@vspo{lqqp$udE5#@2X@f79nEiDfUi9f96u| . -@prefix bp: . -@prefix linkml: . -@prefix owl: . -@prefix rdf: . -@prefix rdfs: . -@prefix skos: . -@prefix xsd: . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - - a owl:Ontology ; - rdfs:label "biological-process-template" ; - IAO:0000700 bp:GeneMolecularActivityRelationship, - , - , - , - , - , - , - ; - linkml:classes "{'BiologicalProcess': ClassDefinition(name='BiologicalProcess', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/biological-process-templateBiologicalProcess', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biological_process', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'biologicalProcess__label', 'biologicalProcess__description', 'biologicalProcess__synonyms', 'biologicalProcess__subclass_of', 'biologicalProcess__inputs', 'biologicalProcess__outputs', 'biologicalProcess__steps', 'biologicalProcess__genes', 'biologicalProcess__gene_activities'], slot_usage={}, attributes={'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='alternative names of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the category to which this biological process belongs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='BiologicalProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'inputs': SlotDefinition(name='inputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the inputs of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'outputs': SlotDefinition(name='outputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the outputs of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'steps': SlotDefinition(name='steps', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the steps involved in this biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_activities': SlotDefinition(name='gene_activities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to molecular activity relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneMolecularActivityRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='bp:BiologicalProcess', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC'], definition_uri='http://w3id.org/ontogpt/biological-process-templateGene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hgnc', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biological_process', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='bp:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'MolecularActivity': ClassDefinition(name='MolecularActivity', id_prefixes=['GO'], definition_uri='http://w3id.org/ontogpt/biological-process-templateMolecularActivity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biological_process', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='bp:MolecularActivity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ChemicalEntity': ClassDefinition(name='ChemicalEntity', id_prefixes=['CHEBI'], definition_uri='http://w3id.org/ontogpt/biological-process-templateChemicalEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:chebi', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biological_process', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='bp:ChemicalEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneMolecularActivityRelationship': ClassDefinition(name='GeneMolecularActivityRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/biological-process-templateGeneMolecularActivityRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biological_process', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneMolecularActivityRelationship__gene', 'geneMolecularActivityRelationship__molecular_activity'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='bp:GeneMolecularActivityRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/biological_process" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -bp:description a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "description" ; - rdfs:range linkml:String ; - skos:definition "a textual description of the biological process" . - -bp:gene a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene" ; - rdfs:range bp:Gene . - -bp:gene_activities a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_activities" ; - rdfs:range bp:GeneMolecularActivityRelationship ; - skos:definition "semicolon-separated list of gene to molecular activity relationships" . - -bp:genes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "genes" ; - rdfs:range bp:Gene . - -bp:inputs a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "inputs" ; - rdfs:range bp:ChemicalEntity ; - skos:definition "the inputs of the biological process" . - -bp:label a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - rdfs:range linkml:String ; - skos:definition "the name of the biological process" . - -bp:molecular_activity a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "molecular_activity" ; - rdfs:range bp:MolecularActivity . - -bp:outputs a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "outputs" ; - rdfs:range bp:ChemicalEntity ; - skos:definition "the outputs of the biological process" . - -bp:steps a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "steps" ; - rdfs:range bp:MolecularActivity ; - skos:definition "the steps involved in this biological process" . - -bp:subclass_of a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subclass_of" ; - rdfs:range bp:BiologicalProcess ; - skos:definition "the category to which this biological process belongs" . - -bp:synonyms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "synonyms" ; - rdfs:range linkml:String ; - skos:definition "alternative names of the biological process" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range ; - skos:definition "The complex objects extracted from the text" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range ; - skos:definition "Named entities extracted from the text" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - bp:prompt.skip "true" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - bp:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch . - - a , - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - - a , - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -bp:BiologicalProcess a owl:Class, - linkml:ClassDefinition ; - rdfs:label "BiologicalProcess" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty bp:label ], - [ a owl:Restriction ; - owl:allValuesFrom bp:ChemicalEntity ; - owl:onProperty bp:outputs ], - [ a owl:Restriction ; - owl:allValuesFrom bp:GeneMolecularActivityRelationship ; - owl:onProperty bp:gene_activities ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty bp:synonyms ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty bp:description ], - [ a owl:Restriction ; - owl:allValuesFrom bp:ChemicalEntity ; - owl:onProperty bp:inputs ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass bp:BiologicalProcess ; - owl:onProperty bp:subclass_of ], - [ a owl:Restriction ; - owl:allValuesFrom bp:MolecularActivity ; - owl:onProperty bp:steps ], - [ a owl:Restriction ; - owl:allValuesFrom bp:Gene ; - owl:onProperty bp:genes ], - ; - linkml:attributes "{'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='alternative names of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the category to which this biological process belongs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='BiologicalProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'inputs': SlotDefinition(name='inputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the inputs of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'outputs': SlotDefinition(name='outputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the outputs of the biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'steps': SlotDefinition(name='steps', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the steps involved in this biological process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_activities': SlotDefinition(name='gene_activities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to molecular activity relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneMolecularActivityRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - - a , - owl:Class ; - rdfs:label "NOT_MENTIONED" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - - a owl:ObjectProperty, - linkml:SlotDefinition . - -bp:GeneMolecularActivityRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneMolecularActivityRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass bp:MolecularActivity ; - owl:onProperty bp:molecular_activity ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass bp:Gene ; - owl:onProperty bp:gene ] ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -bp:ChemicalEntity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalEntity" ; - bp:annotators "sqlite:obo:chebi" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -bp:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - bp:annotators "sqlite:obo:hgnc" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -bp:MolecularActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MolecularActivity" ; - bp:annotators "sqlite:obo:go" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/biological_process/prefixmap/biological_process.yaml b/projects/biological_process/prefixmap/biological_process.yaml deleted file mode 100644 index f6195251e..000000000 --- a/projects/biological_process/prefixmap/biological_process.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{ - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "GO": "http://example.org/UNKNOWN/GO/", - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "bp": "http://w3id.org/ontogpt/biological-process-template", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/biological_process/protobuf/biological_process.proto b/projects/biological_process/protobuf/biological_process.proto deleted file mode 100644 index ae47a2046..000000000 --- a/projects/biological_process/protobuf/biological_process.proto +++ /dev/null @@ -1,68 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message BiologicalProcess - { - string id = 0 - string label = 0 - string description = 0 - repeated string synonyms = 0 - biologicalProcess subclassOf = 0 - repeated chemicalEntity inputs = 0 - repeated chemicalEntity outputs = 0 - repeated molecularActivity steps = 0 - repeated gene genes = 0 - repeated geneMolecularActivityRelationship geneActivities = 0 - } -message ChemicalEntity - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -message GeneMolecularActivityRelationship - { - gene gene = 0 - molecularActivity molecularActivity = 0 - } -message MolecularActivity - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/biological_process/shacl/biological_process.shacl.ttl b/projects/biological_process/shacl/biological_process.shacl.ttl deleted file mode 100644 index 67469826f..000000000 --- a/projects/biological_process/shacl/biological_process.shacl.ttl +++ /dev/null @@ -1,272 +0,0 @@ -@prefix bp: . -@prefix linkml: . -@prefix rdf: . -@prefix sh: . -@prefix xsd: . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path ], - [ sh:class ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path ] ; - sh:targetClass . - -bp:BiologicalProcess a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "alternative names of the biological process" ; - sh:order 2 ; - sh:path bp:synonyms ], - [ sh:class bp:Gene ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path bp:genes ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path ], - [ sh:class bp:ChemicalEntity ; - sh:description "the inputs of the biological process" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path bp:inputs ], - [ sh:class bp:MolecularActivity ; - sh:description "the steps involved in this biological process" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path bp:steps ], - [ sh:description "the name of the biological process" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path bp:label ], - [ sh:class bp:BiologicalProcess ; - sh:description "the category to which this biological process belongs" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path bp:subclass_of ], - [ sh:class bp:GeneMolecularActivityRelationship ; - sh:description "semicolon-separated list of gene to molecular activity relationships" ; - sh:nodeKind sh:BlankNode ; - sh:order 8 ; - sh:path bp:gene_activities ], - [ sh:class bp:ChemicalEntity ; - sh:description "the outputs of the biological process" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path bp:outputs ], - [ sh:description "a textual description of the biological process" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path bp:description ] ; - sh:targetClass bp:BiologicalProcess . - -bp:GeneMolecularActivityRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class bp:MolecularActivity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path bp:molecular_activity ], - [ sh:class bp:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path bp:gene ] ; - sh:targetClass bp:GeneMolecularActivityRelationship . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path ], - [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path ], - [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path ], - [ sh:class ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path ], - [ sh:class ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path ] ; - sh:targetClass . - -bp:ChemicalEntity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass bp:ChemicalEntity . - -bp:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass bp:Gene . - -bp:MolecularActivity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass bp:MolecularActivity . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - - a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - diff --git a/projects/biological_process/shex/biological_process.shex b/projects/biological_process/shex/biological_process.shex deleted file mode 100644 index 2b633d066..000000000 --- a/projects/biological_process/shex/biological_process.shex +++ /dev/null @@ -1,193 +0,0 @@ -BASE -PREFIX rdf: -PREFIX xsd: -PREFIX linkml: -PREFIX core: -PREFIX rdfs1: - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - @linkml:String ? ; - @linkml:String ? ; - @linkml:String * ; - - @ ? ; - - @ * ; - - @ * ; - - @ * ; - @ * ; - - @ * - ) ; - rdf:type [ ] - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - - CLOSED { - ( $ ( - @ ? ; - - @ ? - ) ; - rdf:type [ ] ? - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - -core:NamedEntity ( - @ OR - @ OR - @ OR - @ OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/biological_process/sqlschema/biological_process.sql b/projects/biological_process/sqlschema/biological_process.sql deleted file mode 100644 index 8db0a7bd9..000000000 --- a/projects/biological_process/sqlschema/biological_process.sql +++ /dev/null @@ -1,88 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "BiologicalProcess" ( - id TEXT NOT NULL, - label TEXT, - description TEXT, - subclass_of TEXT, - inputs TEXT, - outputs TEXT, - steps TEXT, - genes TEXT, - PRIMARY KEY (id), - FOREIGN KEY(subclass_of) REFERENCES "BiologicalProcess" (id) -); - -CREATE TABLE "ChemicalEntity" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "MolecularActivity" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "GeneMolecularActivityRelationship" ( - gene TEXT, - molecular_activity TEXT, - "BiologicalProcess_id" TEXT, - PRIMARY KEY (gene, molecular_activity, "BiologicalProcess_id"), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(molecular_activity) REFERENCES "MolecularActivity" (id), - FOREIGN KEY("BiologicalProcess_id") REFERENCES "BiologicalProcess" (id) -); - -CREATE TABLE "BiologicalProcess_synonyms" ( - backref_id TEXT, - synonyms TEXT, - PRIMARY KEY (backref_id, synonyms), - FOREIGN KEY(backref_id) REFERENCES "BiologicalProcess" (id) -); diff --git a/projects/biotic_interaction/biotic_interaction.py b/projects/biotic_interaction/biotic_interaction.py deleted file mode 100644 index c44a7c2a5..000000000 --- a/projects/biotic_interaction/biotic_interaction.py +++ /dev/null @@ -1,475 +0,0 @@ -# Auto generated from biotic_interaction.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:51:35 -# Schema: biotic-interaction-template -# -# id: https://w3id.org/ontogpt/biotic_interaction -# description: A template for biotic interactions -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -COL = CurieNamespace('COL', 'https://www.catalogueoflife.org/data/taxon/') -GBIF = CurieNamespace('GBIF', 'https://www.gbif.org/species/') -ITIS = CurieNamespace('ITIS', 'https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=') -MESH = CurieNamespace('MESH', 'http://example.org/UNKNOWN/MESH/') -NCBITAXON = CurieNamespace('NCBITaxon', 'http://purl.obolibrary.org/obo/NCBITAXON_') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -BP = CurieNamespace('bp', 'http://w3id.org/ontogpt/biotic-interaction-template') -COL = CurieNamespace('col', 'https://www.catalogueoflife.org/data/taxon/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -GBIF = CurieNamespace('gbif', 'https://www.gbif.org/species/') -ITIS = CurieNamespace('itis', 'https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = BP - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class TaxonId(NamedEntityId): - pass - - -class InteractionTypeId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class Container(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.Container - class_class_curie: ClassVar[str] = "bp:Container" - class_name: ClassVar[str] = "Container" - class_model_uri: ClassVar[URIRef] = BP.Container - - interactions: Optional[Union[Union[dict, "BioticInteraction"], List[Union[dict, "BioticInteraction"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.interactions, list): - self.interactions = [self.interactions] if self.interactions is not None else [] - self.interactions = [v if isinstance(v, BioticInteraction) else BioticInteraction(**as_dict(v)) for v in self.interactions] - - super().__post_init__(**kwargs) - - -@dataclass -class BioticInteraction(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.BioticInteraction - class_class_curie: ClassVar[str] = "bp:BioticInteraction" - class_name: ClassVar[str] = "BioticInteraction" - class_model_uri: ClassVar[URIRef] = BP.BioticInteraction - - source_taxon: Optional[Union[str, TaxonId]] = None - target_taxon: Optional[Union[str, TaxonId]] = None - interaction_type: Optional[Union[str, InteractionTypeId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.source_taxon is not None and not isinstance(self.source_taxon, TaxonId): - self.source_taxon = TaxonId(self.source_taxon) - - if self.target_taxon is not None and not isinstance(self.target_taxon, TaxonId): - self.target_taxon = TaxonId(self.target_taxon) - - if self.interaction_type is not None and not isinstance(self.interaction_type, InteractionTypeId): - self.interaction_type = InteractionTypeId(self.interaction_type) - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = BP.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = BP.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Taxon(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.Taxon - class_class_curie: ClassVar[str] = "bp:Taxon" - class_name: ClassVar[str] = "Taxon" - class_model_uri: ClassVar[URIRef] = BP.Taxon - - id: Union[str, TaxonId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, TaxonId): - self.id = TaxonId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class InteractionType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.InteractionType - class_class_curie: ClassVar[str] = "bp:InteractionType" - class_name: ClassVar[str] = "InteractionType" - class_model_uri: ClassVar[URIRef] = BP.InteractionType - - id: Union[str, InteractionTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, InteractionTypeId): - self.id = InteractionTypeId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = BP.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = BP.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = BP.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = BP.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = BP.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = BP.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.container__interactions = Slot(uri=BP.interactions, name="container__interactions", curie=BP.curie('interactions'), - model_uri=BP.container__interactions, domain=None, range=Optional[Union[Union[dict, BioticInteraction], List[Union[dict, BioticInteraction]]]]) - -slots.bioticInteraction__source_taxon = Slot(uri=BP.source_taxon, name="bioticInteraction__source_taxon", curie=BP.curie('source_taxon'), - model_uri=BP.bioticInteraction__source_taxon, domain=None, range=Optional[Union[str, TaxonId]]) - -slots.bioticInteraction__target_taxon = Slot(uri=BP.target_taxon, name="bioticInteraction__target_taxon", curie=BP.curie('target_taxon'), - model_uri=BP.bioticInteraction__target_taxon, domain=None, range=Optional[Union[str, TaxonId]]) - -slots.bioticInteraction__interaction_type = Slot(uri=BP.interaction_type, name="bioticInteraction__interaction_type", curie=BP.curie('interaction_type'), - model_uri=BP.bioticInteraction__interaction_type, domain=None, range=Optional[Union[str, InteractionTypeId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=BP.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=BP.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=BP.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=BP.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=BP.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=BP.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=BP.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=BP.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=BP.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=BP.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=BP.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=BP.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=BP.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=BP.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=BP.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=BP.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=BP.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=BP.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=BP.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=BP.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=BP.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=BP.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=BP.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=BP.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=BP.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/biotic_interaction/docs/AnnotatorResult.md b/projects/biotic_interaction/docs/AnnotatorResult.md deleted file mode 100644 index db84c2ba4..000000000 --- a/projects/biotic_interaction/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [bp:AnnotatorResult](http://w3id.org/ontogpt/biotic-interaction-templateAnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) 0..1 - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) 0..1 - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) 0..1 - * Range: [String](types/String.md) diff --git a/projects/biotic_interaction/docs/Any.md b/projects/biotic_interaction/docs/Any.md deleted file mode 100644 index e75fec3d0..000000000 --- a/projects/biotic_interaction/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [bp:Any](http://w3id.org/ontogpt/biotic-interaction-templateAny) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* 0..1 **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* 0..\* **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/biotic_interaction/docs/BioticInteraction.md b/projects/biotic_interaction/docs/BioticInteraction.md deleted file mode 100644 index d7643307b..000000000 --- a/projects/biotic_interaction/docs/BioticInteraction.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Class: BioticInteraction - - - - -URI: [bp:BioticInteraction](http://w3id.org/ontogpt/biotic-interaction-templateBioticInteraction) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Taxon],[InteractionType],[InteractionType][BioticInteraction],[Container])](https://yuml.me/diagram/nofunky;dir:TB/class/[Taxon],[InteractionType],[InteractionType][BioticInteraction],[Container]) - -## Referenced by Class - - * **None** *[➞interactions](container__interactions.md)* 0..\* **[BioticInteraction](BioticInteraction.md)** - -## Attributes - - -### Own - - * [➞source_taxon](bioticInteraction__source_taxon.md) 0..1 - * Description: the taxon that is the subject of the interaction - * Range: [Taxon](Taxon.md) - * [➞target_taxon](bioticInteraction__target_taxon.md) 0..1 - * Description: the taxon that is the object of the ineteraction - * Range: [Taxon](Taxon.md) - * [➞interaction_type](bioticInteraction__interaction_type.md) 0..1 - * Description: the type of interaction - * Range: [InteractionType](InteractionType.md) diff --git a/projects/biotic_interaction/docs/CompoundExpression.md b/projects/biotic_interaction/docs/CompoundExpression.md deleted file mode 100644 index 9731c53d6..000000000 --- a/projects/biotic_interaction/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [bp:CompoundExpression](http://w3id.org/ontogpt/biotic-interaction-templateCompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/biotic_interaction/docs/Container.md b/projects/biotic_interaction/docs/Container.md deleted file mode 100644 index ff46a8278..000000000 --- a/projects/biotic_interaction/docs/Container.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Class: Container - - - - -URI: [bp:Container](http://w3id.org/ontogpt/biotic-interaction-templateContainer) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[BioticInteraction]0..\* - * Range: [BioticInteraction](BioticInteraction.md) diff --git a/projects/biotic_interaction/docs/ExtractionResult.md b/projects/biotic_interaction/docs/ExtractionResult.md deleted file mode 100644 index 3777dbc52..000000000 --- a/projects/biotic_interaction/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [bp:ExtractionResult](http://w3id.org/ontogpt/biotic-interaction-templateExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]0..1 - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) 0..1 - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) 0..1 - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) 0..1 - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) 0..1 - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) 0..1 - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) 0..\* - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/biotic_interaction/docs/InteractionType.md b/projects/biotic_interaction/docs/InteractionType.md deleted file mode 100644 index a7095cdb4..000000000 --- a/projects/biotic_interaction/docs/InteractionType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: InteractionType - - - - -URI: [bp:InteractionType](http://w3id.org/ontogpt/biotic-interaction-templateInteractionType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BioticInteraction]-%20interaction_type%200..1>[InteractionType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[InteractionType],[BioticInteraction])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[BioticInteraction]-%20interaction_type%200..1>[InteractionType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[InteractionType],[BioticInteraction]) - -## Identifier prefixes - - * RO - * MESH - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞interaction_type](bioticInteraction__interaction_type.md)* 0..1 **[InteractionType](InteractionType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biotic_interaction/docs/NamedEntity.md b/projects/biotic_interaction/docs/NamedEntity.md deleted file mode 100644 index 67f9ded39..000000000 --- a/projects/biotic_interaction/docs/NamedEntity.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [bp:NamedEntity](http://w3id.org/ontogpt/biotic-interaction-templateNamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Taxon],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Taxon],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[InteractionType],[Triple],[InteractionType])](https://yuml.me/diagram/nofunky;dir:TB/class/[Taxon],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Taxon],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[InteractionType],[Triple],[InteractionType]) - -## Children - - * [InteractionType](InteractionType.md) - * [RelationshipType](RelationshipType.md) - * [Taxon](Taxon.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* 0..1 **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biotic_interaction/docs/NullDataOptions.md b/projects/biotic_interaction/docs/NullDataOptions.md deleted file mode 100644 index dedb0768c..000000000 --- a/projects/biotic_interaction/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [bp:NullDataOptions](http://w3id.org/ontogpt/biotic-interaction-templateNullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/biotic_interaction/docs/Publication.md b/projects/biotic_interaction/docs/Publication.md deleted file mode 100644 index af9abc833..000000000 --- a/projects/biotic_interaction/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [bp:Publication](http://w3id.org/ontogpt/biotic-interaction-templatePublication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* 0..1 **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) 0..1 - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) 0..1 - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) 0..1 - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) 0..1 - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) 0..1 - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/biotic_interaction/docs/RelationshipType.md b/projects/biotic_interaction/docs/RelationshipType.md deleted file mode 100644 index 378def0cb..000000000 --- a/projects/biotic_interaction/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [bp:RelationshipType](http://w3id.org/ontogpt/biotic-interaction-templateRelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* 0..1 **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biotic_interaction/docs/Taxon.md b/projects/biotic_interaction/docs/Taxon.md deleted file mode 100644 index d53213fb9..000000000 --- a/projects/biotic_interaction/docs/Taxon.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Class: Taxon - - - - -URI: [bp:Taxon](http://w3id.org/ontogpt/biotic-interaction-templateTaxon) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[BioticInteraction]-%20source_taxon%200..1>[Taxon|id(i):string;label(i):string%20%3F],[BioticInteraction]-%20target_taxon%200..1>[Taxon],[NamedEntity]^-[Taxon],[NamedEntity],[BioticInteraction])](https://yuml.me/diagram/nofunky;dir:TB/class/[BioticInteraction]-%20source_taxon%200..1>[Taxon|id(i):string;label(i):string%20%3F],[BioticInteraction]-%20target_taxon%200..1>[Taxon],[NamedEntity]^-[Taxon],[NamedEntity],[BioticInteraction]) - -## Identifier prefixes - - * NCBITaxon - * COL - * ITIS - * GBIF - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞source_taxon](bioticInteraction__source_taxon.md)* 0..1 **[Taxon](Taxon.md)** - * **None** *[➞target_taxon](bioticInteraction__target_taxon.md)* 0..1 **[Taxon](Taxon.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/biotic_interaction/docs/TextWithTriples.md b/projects/biotic_interaction/docs/TextWithTriples.md deleted file mode 100644 index f7e378a44..000000000 --- a/projects/biotic_interaction/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [bp:TextWithTriples](http://w3id.org/ontogpt/biotic-interaction-templateTextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]0..1 - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) 0..\* - * Range: [Triple](Triple.md) diff --git a/projects/biotic_interaction/docs/Triple.md b/projects/biotic_interaction/docs/Triple.md deleted file mode 100644 index 3024d96ee..000000000 --- a/projects/biotic_interaction/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [bp:Triple](http://w3id.org/ontogpt/biotic-interaction-templateTriple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity][Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity][Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* 0..\* **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) 0..1 - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) 0..1 - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) 0..1 - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) 0..1 - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) 0..1 - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) 0..1 - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/biotic_interaction/docs/annotatorResult__object_id.md b/projects/biotic_interaction/docs/annotatorResult__object_id.md deleted file mode 100644 index 18710c6b5..000000000 --- a/projects/biotic_interaction/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [bp:annotatorResult__object_id](http://w3id.org/ontogpt/biotic-interaction-templateannotatorResult__object_id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/biotic_interaction/docs/annotatorResult__object_text.md b/projects/biotic_interaction/docs/annotatorResult__object_text.md deleted file mode 100644 index d35c5967d..000000000 --- a/projects/biotic_interaction/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [bp:annotatorResult__object_text](http://w3id.org/ontogpt/biotic-interaction-templateannotatorResult__object_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/biotic_interaction/docs/annotatorResult__subject_text.md b/projects/biotic_interaction/docs/annotatorResult__subject_text.md deleted file mode 100644 index 48d7020c1..000000000 --- a/projects/biotic_interaction/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [bp:annotatorResult__subject_text](http://w3id.org/ontogpt/biotic-interaction-templateannotatorResult__subject_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/biotic_interaction/docs/bioticInteraction__interaction_type.md b/projects/biotic_interaction/docs/bioticInteraction__interaction_type.md deleted file mode 100644 index d506fc797..000000000 --- a/projects/biotic_interaction/docs/bioticInteraction__interaction_type.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: interaction_type - - -the type of interaction - -URI: [bp:bioticInteraction__interaction_type](http://w3id.org/ontogpt/biotic-interaction-templatebioticInteraction__interaction_type) - - -## Domain and Range - -None → 0..1 [InteractionType](InteractionType.md) - -## Parents - - -## Children - - -## Used by - - * [BioticInteraction](BioticInteraction.md) diff --git a/projects/biotic_interaction/docs/bioticInteraction__source_taxon.md b/projects/biotic_interaction/docs/bioticInteraction__source_taxon.md deleted file mode 100644 index 0bb5a6319..000000000 --- a/projects/biotic_interaction/docs/bioticInteraction__source_taxon.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: source_taxon - - -the taxon that is the subject of the interaction - -URI: [bp:bioticInteraction__source_taxon](http://w3id.org/ontogpt/biotic-interaction-templatebioticInteraction__source_taxon) - - -## Domain and Range - -None → 0..1 [Taxon](Taxon.md) - -## Parents - - -## Children - - -## Used by - - * [BioticInteraction](BioticInteraction.md) diff --git a/projects/biotic_interaction/docs/bioticInteraction__target_taxon.md b/projects/biotic_interaction/docs/bioticInteraction__target_taxon.md deleted file mode 100644 index f257c11c8..000000000 --- a/projects/biotic_interaction/docs/bioticInteraction__target_taxon.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: target_taxon - - -the taxon that is the object of the ineteraction - -URI: [bp:bioticInteraction__target_taxon](http://w3id.org/ontogpt/biotic-interaction-templatebioticInteraction__target_taxon) - - -## Domain and Range - -None → 0..1 [Taxon](Taxon.md) - -## Parents - - -## Children - - -## Used by - - * [BioticInteraction](BioticInteraction.md) diff --git a/projects/biotic_interaction/docs/biotic_interaction.md b/projects/biotic_interaction/docs/biotic_interaction.md deleted file mode 100644 index 30ad25250..000000000 --- a/projects/biotic_interaction/docs/biotic_interaction.md +++ /dev/null @@ -1,111 +0,0 @@ - -# biotic-interaction-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for biotic interactions - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [BioticInteraction](BioticInteraction.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [Container](Container.md) - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [InteractionType](InteractionType.md) - * [RelationshipType](RelationshipType.md) - * [Taxon](Taxon.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞interaction_type](bioticInteraction__interaction_type.md) - the type of interaction - * [➞source_taxon](bioticInteraction__source_taxon.md) - the taxon that is the subject of the interaction - * [➞target_taxon](bioticInteraction__target_taxon.md) - the taxon that is the object of the ineteraction - * [➞interactions](container__interactions.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/biotic_interaction/docs/container__interactions.md b/projects/biotic_interaction/docs/container__interactions.md deleted file mode 100644 index 414cadbcf..000000000 --- a/projects/biotic_interaction/docs/container__interactions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: interactions - - - - -URI: [bp:container__interactions](http://w3id.org/ontogpt/biotic-interaction-templatecontainer__interactions) - - -## Domain and Range - -None → 0..\* [BioticInteraction](BioticInteraction.md) - -## Parents - - -## Children - - -## Used by - - * [Container](Container.md) diff --git a/projects/biotic_interaction/docs/extractionResult__extracted_object.md b/projects/biotic_interaction/docs/extractionResult__extracted_object.md deleted file mode 100644 index efd3d1c4c..000000000 --- a/projects/biotic_interaction/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [bp:extractionResult__extracted_object](http://w3id.org/ontogpt/biotic-interaction-templateextractionResult__extracted_object) - - -## Domain and Range - -None → 0..1 [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biotic_interaction/docs/extractionResult__input_id.md b/projects/biotic_interaction/docs/extractionResult__input_id.md deleted file mode 100644 index 87ef8b964..000000000 --- a/projects/biotic_interaction/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [bp:extractionResult__input_id](http://w3id.org/ontogpt/biotic-interaction-templateextractionResult__input_id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biotic_interaction/docs/extractionResult__input_text.md b/projects/biotic_interaction/docs/extractionResult__input_text.md deleted file mode 100644 index f193ada62..000000000 --- a/projects/biotic_interaction/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [bp:extractionResult__input_text](http://w3id.org/ontogpt/biotic-interaction-templateextractionResult__input_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biotic_interaction/docs/extractionResult__input_title.md b/projects/biotic_interaction/docs/extractionResult__input_title.md deleted file mode 100644 index c663e1e7e..000000000 --- a/projects/biotic_interaction/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [bp:extractionResult__input_title](http://w3id.org/ontogpt/biotic-interaction-templateextractionResult__input_title) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biotic_interaction/docs/extractionResult__named_entities.md b/projects/biotic_interaction/docs/extractionResult__named_entities.md deleted file mode 100644 index 68c893212..000000000 --- a/projects/biotic_interaction/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [bp:extractionResult__named_entities](http://w3id.org/ontogpt/biotic-interaction-templateextractionResult__named_entities) - - -## Domain and Range - -None → 0..\* [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biotic_interaction/docs/extractionResult__prompt.md b/projects/biotic_interaction/docs/extractionResult__prompt.md deleted file mode 100644 index 78879550a..000000000 --- a/projects/biotic_interaction/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [bp:extractionResult__prompt](http://w3id.org/ontogpt/biotic-interaction-templateextractionResult__prompt) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biotic_interaction/docs/extractionResult__raw_completion_output.md b/projects/biotic_interaction/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 9b6e6e45e..000000000 --- a/projects/biotic_interaction/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [bp:extractionResult__raw_completion_output](http://w3id.org/ontogpt/biotic-interaction-templateextractionResult__raw_completion_output) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/biotic_interaction/docs/namedEntity__id.md b/projects/biotic_interaction/docs/namedEntity__id.md deleted file mode 100644 index 14356b649..000000000 --- a/projects/biotic_interaction/docs/namedEntity__id.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [bp:namedEntity__id](http://w3id.org/ontogpt/biotic-interaction-templatenamedEntity__id) - - -## Domain and Range - -None → 1..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [InteractionType](InteractionType.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Taxon](Taxon.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/biotic_interaction/docs/namedEntity__label.md b/projects/biotic_interaction/docs/namedEntity__label.md deleted file mode 100644 index cde2f631a..000000000 --- a/projects/biotic_interaction/docs/namedEntity__label.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [bp:namedEntity__label](http://w3id.org/ontogpt/biotic-interaction-templatenamedEntity__label) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [InteractionType](InteractionType.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Taxon](Taxon.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/biotic_interaction/docs/publication__abstract.md b/projects/biotic_interaction/docs/publication__abstract.md deleted file mode 100644 index af0167b2a..000000000 --- a/projects/biotic_interaction/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [bp:publication__abstract](http://w3id.org/ontogpt/biotic-interaction-templatepublication__abstract) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biotic_interaction/docs/publication__combined_text.md b/projects/biotic_interaction/docs/publication__combined_text.md deleted file mode 100644 index b72ba43fd..000000000 --- a/projects/biotic_interaction/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [bp:publication__combined_text](http://w3id.org/ontogpt/biotic-interaction-templatepublication__combined_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biotic_interaction/docs/publication__full_text.md b/projects/biotic_interaction/docs/publication__full_text.md deleted file mode 100644 index 88567808f..000000000 --- a/projects/biotic_interaction/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [bp:publication__full_text](http://w3id.org/ontogpt/biotic-interaction-templatepublication__full_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biotic_interaction/docs/publication__id.md b/projects/biotic_interaction/docs/publication__id.md deleted file mode 100644 index 3e49e00d9..000000000 --- a/projects/biotic_interaction/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [bp:publication__id](http://w3id.org/ontogpt/biotic-interaction-templatepublication__id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biotic_interaction/docs/publication__title.md b/projects/biotic_interaction/docs/publication__title.md deleted file mode 100644 index 2c6e2030a..000000000 --- a/projects/biotic_interaction/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [bp:publication__title](http://w3id.org/ontogpt/biotic-interaction-templatepublication__title) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/biotic_interaction/docs/textWithTriples__publication.md b/projects/biotic_interaction/docs/textWithTriples__publication.md deleted file mode 100644 index 704695d79..000000000 --- a/projects/biotic_interaction/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [bp:textWithTriples__publication](http://w3id.org/ontogpt/biotic-interaction-templatetextWithTriples__publication) - - -## Domain and Range - -None → 0..1 [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/biotic_interaction/docs/textWithTriples__triples.md b/projects/biotic_interaction/docs/textWithTriples__triples.md deleted file mode 100644 index fd4d50e1d..000000000 --- a/projects/biotic_interaction/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [bp:textWithTriples__triples](http://w3id.org/ontogpt/biotic-interaction-templatetextWithTriples__triples) - - -## Domain and Range - -None → 0..\* [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/biotic_interaction/docs/triple__object.md b/projects/biotic_interaction/docs/triple__object.md deleted file mode 100644 index 30f531cf8..000000000 --- a/projects/biotic_interaction/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [bp:triple__object](http://w3id.org/ontogpt/biotic-interaction-templatetriple__object) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biotic_interaction/docs/triple__object_qualifier.md b/projects/biotic_interaction/docs/triple__object_qualifier.md deleted file mode 100644 index 12af0c071..000000000 --- a/projects/biotic_interaction/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [bp:triple__object_qualifier](http://w3id.org/ontogpt/biotic-interaction-templatetriple__object_qualifier) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biotic_interaction/docs/triple__predicate.md b/projects/biotic_interaction/docs/triple__predicate.md deleted file mode 100644 index 4ef988d55..000000000 --- a/projects/biotic_interaction/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [bp:triple__predicate](http://w3id.org/ontogpt/biotic-interaction-templatetriple__predicate) - - -## Domain and Range - -None → 0..1 [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biotic_interaction/docs/triple__qualifier.md b/projects/biotic_interaction/docs/triple__qualifier.md deleted file mode 100644 index 7794cfcdf..000000000 --- a/projects/biotic_interaction/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [bp:triple__qualifier](http://w3id.org/ontogpt/biotic-interaction-templatetriple__qualifier) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biotic_interaction/docs/triple__subject.md b/projects/biotic_interaction/docs/triple__subject.md deleted file mode 100644 index 9571ca4d5..000000000 --- a/projects/biotic_interaction/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [bp:triple__subject](http://w3id.org/ontogpt/biotic-interaction-templatetriple__subject) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biotic_interaction/docs/triple__subject_qualifier.md b/projects/biotic_interaction/docs/triple__subject_qualifier.md deleted file mode 100644 index ed6d2dbff..000000000 --- a/projects/biotic_interaction/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [bp:triple__subject_qualifier](http://w3id.org/ontogpt/biotic-interaction-templatetriple__subject_qualifier) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/biotic_interaction/docs/types/Boolean.md b/projects/biotic_interaction/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/biotic_interaction/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/biotic_interaction/docs/types/Curie.md b/projects/biotic_interaction/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/biotic_interaction/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/biotic_interaction/docs/types/Date.md b/projects/biotic_interaction/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/biotic_interaction/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/biotic_interaction/docs/types/DateOrDatetime.md b/projects/biotic_interaction/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/biotic_interaction/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/biotic_interaction/docs/types/Datetime.md b/projects/biotic_interaction/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/biotic_interaction/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/biotic_interaction/docs/types/Decimal.md b/projects/biotic_interaction/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/biotic_interaction/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/biotic_interaction/docs/types/Double.md b/projects/biotic_interaction/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/biotic_interaction/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/biotic_interaction/docs/types/Float.md b/projects/biotic_interaction/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/biotic_interaction/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/biotic_interaction/docs/types/Integer.md b/projects/biotic_interaction/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/biotic_interaction/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/biotic_interaction/docs/types/Jsonpath.md b/projects/biotic_interaction/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/biotic_interaction/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/biotic_interaction/docs/types/Jsonpointer.md b/projects/biotic_interaction/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/biotic_interaction/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/biotic_interaction/docs/types/Ncname.md b/projects/biotic_interaction/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/biotic_interaction/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/biotic_interaction/docs/types/Nodeidentifier.md b/projects/biotic_interaction/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/biotic_interaction/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/biotic_interaction/docs/types/Objectidentifier.md b/projects/biotic_interaction/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/biotic_interaction/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/biotic_interaction/docs/types/Sparqlpath.md b/projects/biotic_interaction/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/biotic_interaction/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/biotic_interaction/docs/types/String.md b/projects/biotic_interaction/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/biotic_interaction/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/biotic_interaction/docs/types/Time.md b/projects/biotic_interaction/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/biotic_interaction/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/biotic_interaction/docs/types/Uri.md b/projects/biotic_interaction/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/biotic_interaction/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/biotic_interaction/docs/types/Uriorcurie.md b/projects/biotic_interaction/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/biotic_interaction/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/biotic_interaction/excel/biotic_interaction.xlsx b/projects/biotic_interaction/excel/biotic_interaction.xlsx deleted file mode 100644 index 24422f1cb577db91a79a3a29d25d1f77e85fd31f..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 9183 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, - , - , - , - , - ; - linkml:classes "{'Container': ClassDefinition(name='Container', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/biotic-interaction-templateContainer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biotic_interaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['container__interactions'], slot_usage={}, attributes={'interactions': SlotDefinition(name='interactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='BioticInteraction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='bp:Container', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'BioticInteraction': ClassDefinition(name='BioticInteraction', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/biotic-interaction-templateBioticInteraction', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='A semi-colon separated list of taxon to taxon relationships', extensions={}, annotations={}), 'prompt.example': Annotation(tag='prompt.example', value='Carcharodon carcharias eats elephant seal; Pandarus sinuatus parasitizes Carcharodon carcharias; orca eats Carcharodon carcharias', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biotic_interaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['bioticInteraction__source_taxon', 'bioticInteraction__target_taxon', 'bioticInteraction__interaction_type'], slot_usage={}, attributes={'source_taxon': SlotDefinition(name='source_taxon', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the taxon that is the subject of the interaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'target_taxon': SlotDefinition(name='target_taxon', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the taxon that is the object of the ineteraction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'interaction_type': SlotDefinition(name='interaction_type', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the type of interaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='InteractionType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='bp:BioticInteraction', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Taxon': ClassDefinition(name='Taxon', id_prefixes=['NCBITaxon', 'COL', 'ITIS', 'GBIF'], definition_uri='http://w3id.org/ontogpt/biotic-interaction-templateTaxon', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:ncbitaxon', extensions={}, annotations={}), 'prompt.example': Annotation(tag='prompt.example', value='shark, Carcharodon carcharias, elephant seal, Pandarus sinuatus, orca', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biotic_interaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='bp:Taxon', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'InteractionType': ClassDefinition(name='InteractionType', id_prefixes=['RO', 'MESH'], definition_uri='http://w3id.org/ontogpt/biotic-interaction-templateInteractionType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:ro, sqlite:obo:bero', extensions={}, annotations={}), 'prompt.example': Annotation(tag='prompt.example', value='eats, competes with, parasitizes', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/biotic_interaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='bp:InteractionType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/biotic_interaction" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -bp:Container a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Container" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom bp:BioticInteraction ; - owl:onProperty bp:interactions ] ; - linkml:attributes "{'interactions': SlotDefinition(name='interactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='BioticInteraction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -bp:interaction_type a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "interaction_type" ; - rdfs:range bp:InteractionType ; - skos:definition "the type of interaction" . - -bp:interactions a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "interactions" ; - rdfs:range bp:BioticInteraction . - -bp:source_taxon a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "source_taxon" ; - rdfs:range bp:Taxon ; - skos:definition "the taxon that is the subject of the interaction" . - -bp:target_taxon a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "target_taxon" ; - rdfs:range bp:Taxon ; - skos:definition "the taxon that is the object of the ineteraction" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range ; - skos:definition "The complex objects extracted from the text" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range ; - skos:definition "Named entities extracted from the text" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - bp:prompt.skip "true" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - bp:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch . - - a , - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - - a , - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -bp:InteractionType a owl:Class, - linkml:ClassDefinition ; - rdfs:label "InteractionType" ; - bp:annotators "sqlite:obo:go, sqlite:obo:ro, sqlite:obo:bero" ; - bp:prompt.example "eats, competes with, parasitizes" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - - a , - owl:Class ; - rdfs:label "NOT_MENTIONED" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - - a owl:ObjectProperty, - linkml:SlotDefinition . - -bp:BioticInteraction a owl:Class, - linkml:ClassDefinition ; - rdfs:label "BioticInteraction" ; - bp:prompt "A semi-colon separated list of taxon to taxon relationships" ; - bp:prompt.example "Carcharodon carcharias eats elephant seal; Pandarus sinuatus parasitizes Carcharodon carcharias; orca eats Carcharodon carcharias" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass bp:Taxon ; - owl:onProperty bp:source_taxon ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass bp:InteractionType ; - owl:onProperty bp:interaction_type ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass bp:Taxon ; - owl:onProperty bp:target_taxon ] ; - linkml:attributes "{'source_taxon': SlotDefinition(name='source_taxon', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the taxon that is the subject of the interaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'target_taxon': SlotDefinition(name='target_taxon', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the taxon that is the object of the ineteraction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Taxon', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'interaction_type': SlotDefinition(name='interaction_type', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the type of interaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='InteractionType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -bp:Taxon a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Taxon" ; - bp:annotators "sqlite:obo:ncbitaxon" ; - bp:prompt.example "shark, Carcharodon carcharias, elephant seal, Pandarus sinuatus, orca" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/biotic_interaction/prefixmap/biotic_interaction.yaml b/projects/biotic_interaction/prefixmap/biotic_interaction.yaml deleted file mode 100644 index 1c2b0a907..000000000 --- a/projects/biotic_interaction/prefixmap/biotic_interaction.yaml +++ /dev/null @@ -1,43 +0,0 @@ -{ - "COL": "https://www.catalogueoflife.org/data/taxon/", - "GBIF": "https://www.gbif.org/species/", - "ITIS": "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=", - "MESH": "http://example.org/UNKNOWN/MESH/", - "NCBITaxon": "http://purl.obolibrary.org/obo/NCBITAXON_", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "bp": "http://w3id.org/ontogpt/biotic-interaction-template", - "col": "https://www.catalogueoflife.org/data/taxon/", - "core": "http://w3id.org/ontogpt/core/", - "gbif": "https://www.gbif.org/species/", - "itis": "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/biotic_interaction/protobuf/biotic_interaction.proto b/projects/biotic_interaction/protobuf/biotic_interaction.proto deleted file mode 100644 index 942fa12b1..000000000 --- a/projects/biotic_interaction/protobuf/biotic_interaction.proto +++ /dev/null @@ -1,55 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message BioticInteraction - { - taxon sourceTaxon = 0 - taxon targetTaxon = 0 - interactionType interactionType = 0 - } -message Container - { - repeated bioticInteraction interactions = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message InteractionType - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message Taxon - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/biotic_interaction/shacl/biotic_interaction.shacl.ttl b/projects/biotic_interaction/shacl/biotic_interaction.shacl.ttl deleted file mode 100644 index 9f58c3138..000000000 --- a/projects/biotic_interaction/shacl/biotic_interaction.shacl.ttl +++ /dev/null @@ -1,224 +0,0 @@ -@prefix bp: . -@prefix linkml: . -@prefix rdf: . -@prefix sh: . -@prefix xsd: . - -bp:Container a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class bp:BioticInteraction ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path bp:interactions ] ; - sh:targetClass bp:Container . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path ], - [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - -bp:BioticInteraction a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class bp:InteractionType ; - sh:description "the type of interaction" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path bp:interaction_type ], - [ sh:class bp:Taxon ; - sh:description "the taxon that is the subject of the interaction" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path bp:source_taxon ], - [ sh:class bp:Taxon ; - sh:description "the taxon that is the object of the ineteraction" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path bp:target_taxon ] ; - sh:targetClass bp:BioticInteraction . - -bp:InteractionType a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass bp:InteractionType . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path ], - [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path ], - [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path ], - [ sh:class ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path ], - [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path ] ; - sh:targetClass . - -bp:Taxon a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass bp:Taxon . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - - a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - diff --git a/projects/biotic_interaction/shex/biotic_interaction.shex b/projects/biotic_interaction/shex/biotic_interaction.shex deleted file mode 100644 index e48f21968..000000000 --- a/projects/biotic_interaction/shex/biotic_interaction.shex +++ /dev/null @@ -1,172 +0,0 @@ -BASE -PREFIX rdf: -PREFIX xsd: -PREFIX linkml: -PREFIX core: -PREFIX rdfs1: - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - - CLOSED { - ( $ ( - - @ ? ; - - @ ? ; - - @ ? - ) ; - rdf:type [ ] ? - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - - CLOSED { - ( $ - - @ * ; - rdf:type [ ] ? - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - -core:NamedEntity ( - @ OR @core:RelationshipType OR - @ -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/biotic_interaction/sqlschema/biotic_interaction.sql b/projects/biotic_interaction/sqlschema/biotic_interaction.sql deleted file mode 100644 index 28357915d..000000000 --- a/projects/biotic_interaction/sqlschema/biotic_interaction.sql +++ /dev/null @@ -1,67 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Container" ( - interactions TEXT, - PRIMARY KEY (interactions) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "InteractionType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Taxon" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "BioticInteraction" ( - source_taxon TEXT, - target_taxon TEXT, - interaction_type TEXT, - PRIMARY KEY (source_taxon, target_taxon, interaction_type), - FOREIGN KEY(source_taxon) REFERENCES "Taxon" (id), - FOREIGN KEY(target_taxon) REFERENCES "Taxon" (id), - FOREIGN KEY(interaction_type) REFERENCES "InteractionType" (id) -); diff --git a/projects/class_enrichment/class_enrichment.py b/projects/class_enrichment/class_enrichment.py deleted file mode 100644 index 74d0538c3..000000000 --- a/projects/class_enrichment/class_enrichment.py +++ /dev/null @@ -1,249 +0,0 @@ -# Auto generated from class_enrichment.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:51:45 -# Schema: class-enrichment -# -# id: https://w3id.org/oak/class-enrichment -# description: A datamodel for representing the results of class enrichment on gene sets -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import Boolean, Float, Integer, String, Uriorcurie -from linkml_runtime.utils.metamodelcore import Bool, URIorCURIE - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -OBI = CurieNamespace('OBI', 'http://purl.obolibrary.org/obo/OBI_') -STATO = CurieNamespace('STATO', 'http://purl.obolibrary.org/obo/STATO_') -BPA = CurieNamespace('bpa', 'https://bioportal.bioontology.org/annotator/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -OA = CurieNamespace('oa', 'http://www.w3.org/ns/oa#') -ONTOENRICH = CurieNamespace('ontoenrich', 'https://w3id.org/oak/class-enrichment/') -OWL = CurieNamespace('owl', 'http://www.w3.org/2002/07/owl#') -PAV = CurieNamespace('pav', 'http://purl.org/pav/') -PROV = CurieNamespace('prov', 'http://www.w3.org/ns/prov#') -RDF = CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#') -RDFS = CurieNamespace('rdfs', 'http://www.w3.org/2000/01/rdf-schema#') -SCHEMA = CurieNamespace('schema', 'http://schema.org/') -SH = CurieNamespace('sh', 'https://w3id.org/shacl/') -SKOS = CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#') -SSSOM = CurieNamespace('sssom', 'http://w3id.org/sssom/') -XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#') -DEFAULT_ = ONTOENRICH - - -# Types -class Position(Integer): - type_class_uri = XSD.integer - type_class_curie = "xsd:integer" - type_name = "Position" - type_model_uri = ONTOENRICH.Position - - -# Class references - - - -@dataclass -class ClassEnrichmentConfiguration(YAMLRoot): - """ - configuration for search - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ONTOENRICH.ClassEnrichmentConfiguration - class_class_curie: ClassVar[str] = "ontoenrich:ClassEnrichmentConfiguration" - class_name: ClassVar[str] = "ClassEnrichmentConfiguration" - class_model_uri: ClassVar[URIRef] = ONTOENRICH.ClassEnrichmentConfiguration - - p_value_cutoff: float = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.p_value_cutoff): - self.MissingRequiredField("p_value_cutoff") - if not isinstance(self.p_value_cutoff, float): - self.p_value_cutoff = float(self.p_value_cutoff) - - super().__post_init__(**kwargs) - - -@dataclass -class ClassEnrichmentResultSet(YAMLRoot): - """ - A collection of enrichemt results - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ONTOENRICH.ClassEnrichmentResultSet - class_class_curie: ClassVar[str] = "ontoenrich:ClassEnrichmentResultSet" - class_name: ClassVar[str] = "ClassEnrichmentResultSet" - class_model_uri: ClassVar[URIRef] = ONTOENRICH.ClassEnrichmentResultSet - - results: Optional[Union[Union[dict, "ClassEnrichmentResult"], List[Union[dict, "ClassEnrichmentResult"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - self._normalize_inlined_as_dict(slot_name="results", slot_type=ClassEnrichmentResult, key_name="class_id", keyed=False) - - super().__post_init__(**kwargs) - - -@dataclass -class ClassEnrichmentResult(YAMLRoot): - """ - A single enrichment result - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ONTOENRICH.ClassEnrichmentResult - class_class_curie: ClassVar[str] = "ontoenrich:ClassEnrichmentResult" - class_name: ClassVar[str] = "ClassEnrichmentResult" - class_model_uri: ClassVar[URIRef] = ONTOENRICH.ClassEnrichmentResult - - class_id: Union[str, URIorCURIE] = None - p_value: float = None - class_label: Optional[str] = None - rank: Optional[int] = None - p_value_adjusted: Optional[float] = None - false_discovery_rate: Optional[float] = None - fold_enrichment: Optional[float] = None - probability: Optional[float] = None - sample_count: Optional[int] = None - sample_total: Optional[int] = None - background_count: Optional[int] = None - background_total: Optional[int] = None - ancestor_of_more_informative_result: Optional[Union[bool, Bool]] = None - descendant_of_more_informative_result: Optional[Union[bool, Bool]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.class_id): - self.MissingRequiredField("class_id") - if not isinstance(self.class_id, URIorCURIE): - self.class_id = URIorCURIE(self.class_id) - - if self._is_empty(self.p_value): - self.MissingRequiredField("p_value") - if not isinstance(self.p_value, float): - self.p_value = float(self.p_value) - - if self.class_label is not None and not isinstance(self.class_label, str): - self.class_label = str(self.class_label) - - if self.rank is not None and not isinstance(self.rank, int): - self.rank = int(self.rank) - - if self.p_value_adjusted is not None and not isinstance(self.p_value_adjusted, float): - self.p_value_adjusted = float(self.p_value_adjusted) - - if self.false_discovery_rate is not None and not isinstance(self.false_discovery_rate, float): - self.false_discovery_rate = float(self.false_discovery_rate) - - if self.fold_enrichment is not None and not isinstance(self.fold_enrichment, float): - self.fold_enrichment = float(self.fold_enrichment) - - if self.probability is not None and not isinstance(self.probability, float): - self.probability = float(self.probability) - - if self.sample_count is not None and not isinstance(self.sample_count, int): - self.sample_count = int(self.sample_count) - - if self.sample_total is not None and not isinstance(self.sample_total, int): - self.sample_total = int(self.sample_total) - - if self.background_count is not None and not isinstance(self.background_count, int): - self.background_count = int(self.background_count) - - if self.background_total is not None and not isinstance(self.background_total, int): - self.background_total = int(self.background_total) - - if self.ancestor_of_more_informative_result is not None and not isinstance(self.ancestor_of_more_informative_result, Bool): - self.ancestor_of_more_informative_result = Bool(self.ancestor_of_more_informative_result) - - if self.descendant_of_more_informative_result is not None and not isinstance(self.descendant_of_more_informative_result, Bool): - self.descendant_of_more_informative_result = Bool(self.descendant_of_more_informative_result) - - super().__post_init__(**kwargs) - - -# Enumerations -class SortFieldEnum(EnumDefinitionImpl): - """ - The field to sort by - """ - ANY = PermissibleValue(text="ANY") - P_VALUE = PermissibleValue(text="P_VALUE") - - _defn = EnumDefinition( - name="SortFieldEnum", - description="The field to sort by", - ) - -# Slots -class slots: - pass - -slots.classEnrichmentConfiguration__p_value_cutoff = Slot(uri=ONTOENRICH.p_value_cutoff, name="classEnrichmentConfiguration__p_value_cutoff", curie=ONTOENRICH.curie('p_value_cutoff'), - model_uri=ONTOENRICH.classEnrichmentConfiguration__p_value_cutoff, domain=None, range=float) - -slots.classEnrichmentResultSet__results = Slot(uri=ONTOENRICH.results, name="classEnrichmentResultSet__results", curie=ONTOENRICH.curie('results'), - model_uri=ONTOENRICH.classEnrichmentResultSet__results, domain=None, range=Optional[Union[Union[dict, ClassEnrichmentResult], List[Union[dict, ClassEnrichmentResult]]]]) - -slots.classEnrichmentResult__class_id = Slot(uri=ONTOENRICH.class_id, name="classEnrichmentResult__class_id", curie=ONTOENRICH.curie('class_id'), - model_uri=ONTOENRICH.classEnrichmentResult__class_id, domain=None, range=Union[str, URIorCURIE]) - -slots.classEnrichmentResult__class_label = Slot(uri=ONTOENRICH.class_label, name="classEnrichmentResult__class_label", curie=ONTOENRICH.curie('class_label'), - model_uri=ONTOENRICH.classEnrichmentResult__class_label, domain=None, range=Optional[str]) - -slots.classEnrichmentResult__rank = Slot(uri=ONTOENRICH.rank, name="classEnrichmentResult__rank", curie=ONTOENRICH.curie('rank'), - model_uri=ONTOENRICH.classEnrichmentResult__rank, domain=None, range=Optional[int]) - -slots.classEnrichmentResult__p_value = Slot(uri=OBI['0000175'], name="classEnrichmentResult__p_value", curie=OBI.curie('0000175'), - model_uri=ONTOENRICH.classEnrichmentResult__p_value, domain=None, range=float) - -slots.classEnrichmentResult__p_value_adjusted = Slot(uri=ONTOENRICH.p_value_adjusted, name="classEnrichmentResult__p_value_adjusted", curie=ONTOENRICH.curie('p_value_adjusted'), - model_uri=ONTOENRICH.classEnrichmentResult__p_value_adjusted, domain=None, range=Optional[float]) - -slots.classEnrichmentResult__false_discovery_rate = Slot(uri=ONTOENRICH.false_discovery_rate, name="classEnrichmentResult__false_discovery_rate", curie=ONTOENRICH.curie('false_discovery_rate'), - model_uri=ONTOENRICH.classEnrichmentResult__false_discovery_rate, domain=None, range=Optional[float]) - -slots.classEnrichmentResult__fold_enrichment = Slot(uri=ONTOENRICH.fold_enrichment, name="classEnrichmentResult__fold_enrichment", curie=ONTOENRICH.curie('fold_enrichment'), - model_uri=ONTOENRICH.classEnrichmentResult__fold_enrichment, domain=None, range=Optional[float]) - -slots.classEnrichmentResult__probability = Slot(uri=ONTOENRICH.probability, name="classEnrichmentResult__probability", curie=ONTOENRICH.curie('probability'), - model_uri=ONTOENRICH.classEnrichmentResult__probability, domain=None, range=Optional[float]) - -slots.classEnrichmentResult__sample_count = Slot(uri=ONTOENRICH.sample_count, name="classEnrichmentResult__sample_count", curie=ONTOENRICH.curie('sample_count'), - model_uri=ONTOENRICH.classEnrichmentResult__sample_count, domain=None, range=Optional[int]) - -slots.classEnrichmentResult__sample_total = Slot(uri=ONTOENRICH.sample_total, name="classEnrichmentResult__sample_total", curie=ONTOENRICH.curie('sample_total'), - model_uri=ONTOENRICH.classEnrichmentResult__sample_total, domain=None, range=Optional[int]) - -slots.classEnrichmentResult__background_count = Slot(uri=ONTOENRICH.background_count, name="classEnrichmentResult__background_count", curie=ONTOENRICH.curie('background_count'), - model_uri=ONTOENRICH.classEnrichmentResult__background_count, domain=None, range=Optional[int]) - -slots.classEnrichmentResult__background_total = Slot(uri=ONTOENRICH.background_total, name="classEnrichmentResult__background_total", curie=ONTOENRICH.curie('background_total'), - model_uri=ONTOENRICH.classEnrichmentResult__background_total, domain=None, range=Optional[int]) - -slots.classEnrichmentResult__ancestor_of_more_informative_result = Slot(uri=ONTOENRICH.ancestor_of_more_informative_result, name="classEnrichmentResult__ancestor_of_more_informative_result", curie=ONTOENRICH.curie('ancestor_of_more_informative_result'), - model_uri=ONTOENRICH.classEnrichmentResult__ancestor_of_more_informative_result, domain=None, range=Optional[Union[bool, Bool]]) - -slots.classEnrichmentResult__descendant_of_more_informative_result = Slot(uri=ONTOENRICH.descendant_of_more_informative_result, name="classEnrichmentResult__descendant_of_more_informative_result", curie=ONTOENRICH.curie('descendant_of_more_informative_result'), - model_uri=ONTOENRICH.classEnrichmentResult__descendant_of_more_informative_result, domain=None, range=Optional[Union[bool, Bool]]) \ No newline at end of file diff --git a/projects/class_enrichment/docs/ClassEnrichmentConfiguration.md b/projects/class_enrichment/docs/ClassEnrichmentConfiguration.md deleted file mode 100644 index bc480f79b..000000000 --- a/projects/class_enrichment/docs/ClassEnrichmentConfiguration.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Class: ClassEnrichmentConfiguration - - -configuration for search - -URI: [ontoenrich:ClassEnrichmentConfiguration](https://w3id.org/oak/class-enrichment/ClassEnrichmentConfiguration) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ClassEnrichmentConfiguration|p_value_cutoff:float])](https://yuml.me/diagram/nofunky;dir:TB/class/[ClassEnrichmentConfiguration|p_value_cutoff:float]) - -## Attributes - - -### Own - - * [➞p_value_cutoff](classEnrichmentConfiguration__p_value_cutoff.md) 1..1 - * Description: p-value cutoff for enrichment - * Range: [Float](types/Float.md) diff --git a/projects/class_enrichment/docs/ClassEnrichmentResult.md b/projects/class_enrichment/docs/ClassEnrichmentResult.md deleted file mode 100644 index b39918d32..000000000 --- a/projects/class_enrichment/docs/ClassEnrichmentResult.md +++ /dev/null @@ -1,62 +0,0 @@ - -# Class: ClassEnrichmentResult - - -A single enrichment result - -URI: [ontoenrich:ClassEnrichmentResult](https://w3id.org/oak/class-enrichment/ClassEnrichmentResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ClassEnrichmentResultSet]++-%20results%200..*>[ClassEnrichmentResult|class_id:uriorcurie;class_label:string%20%3F;rank:integer%20%3F;p_value:float;p_value_adjusted:float%20%3F;false_discovery_rate:float%20%3F;fold_enrichment:float%20%3F;probability:float%20%3F;sample_count:integer%20%3F;sample_total:integer%20%3F;background_count:integer%20%3F;background_total:integer%20%3F;ancestor_of_more_informative_result:boolean%20%3F;descendant_of_more_informative_result:boolean%20%3F],[ClassEnrichmentResultSet])](https://yuml.me/diagram/nofunky;dir:TB/class/[ClassEnrichmentResultSet]++-%20results%200..*>[ClassEnrichmentResult|class_id:uriorcurie;class_label:string%20%3F;rank:integer%20%3F;p_value:float;p_value_adjusted:float%20%3F;false_discovery_rate:float%20%3F;fold_enrichment:float%20%3F;probability:float%20%3F;sample_count:integer%20%3F;sample_total:integer%20%3F;background_count:integer%20%3F;background_total:integer%20%3F;ancestor_of_more_informative_result:boolean%20%3F;descendant_of_more_informative_result:boolean%20%3F],[ClassEnrichmentResultSet]) - -## Referenced by Class - - * **None** *[➞results](classEnrichmentResultSet__results.md)* 0..\* **[ClassEnrichmentResult](ClassEnrichmentResult.md)** - -## Attributes - - -### Own - - * [➞class_id](classEnrichmentResult__class_id.md) 1..1 - * Description: The class id - * Range: [Uriorcurie](types/Uriorcurie.md) - * [➞class_label](classEnrichmentResult__class_label.md) 0..1 - * Description: The class label - * Range: [String](types/String.md) - * [➞rank](classEnrichmentResult__rank.md) 0..1 - * Description: The rank of this result - * Range: [Integer](types/Integer.md) - * [➞p_value](classEnrichmentResult__p_value.md) 1..1 - * Description: The p-value - * Range: [Float](types/Float.md) - * [➞p_value_adjusted](classEnrichmentResult__p_value_adjusted.md) 0..1 - * Description: The adjusted p-value - * Range: [Float](types/Float.md) - * [➞false_discovery_rate](classEnrichmentResult__false_discovery_rate.md) 0..1 - * Description: The false discovery rate - * Range: [Float](types/Float.md) - * [➞fold_enrichment](classEnrichmentResult__fold_enrichment.md) 0..1 - * Description: The fold enrichment - * Range: [Float](types/Float.md) - * [➞probability](classEnrichmentResult__probability.md) 0..1 - * Description: The probability, as estimated by model-based approaches - * Range: [Float](types/Float.md) - * [➞sample_count](classEnrichmentResult__sample_count.md) 0..1 - * Description: The number of entities in the sample with this class - * Range: [Integer](types/Integer.md) - * [➞sample_total](classEnrichmentResult__sample_total.md) 0..1 - * Description: The total number of entities in the sample - * Range: [Integer](types/Integer.md) - * [➞background_count](classEnrichmentResult__background_count.md) 0..1 - * Description: The background count - * Range: [Integer](types/Integer.md) - * [➞background_total](classEnrichmentResult__background_total.md) 0..1 - * Description: The background total - * Range: [Integer](types/Integer.md) - * [➞ancestor_of_more_informative_result](classEnrichmentResult__ancestor_of_more_informative_result.md) 0..1 - * Description: This term is more general than a previously reported result - * Range: [Boolean](types/Boolean.md) - * [➞descendant_of_more_informative_result](classEnrichmentResult__descendant_of_more_informative_result.md) 0..1 - * Description: This term is more specific than a previously reported result - * Range: [Boolean](types/Boolean.md) diff --git a/projects/class_enrichment/docs/ClassEnrichmentResultSet.md b/projects/class_enrichment/docs/ClassEnrichmentResultSet.md deleted file mode 100644 index 984538cf5..000000000 --- a/projects/class_enrichment/docs/ClassEnrichmentResultSet.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Class: ClassEnrichmentResultSet - - -A collection of enrichemt results - -URI: [ontoenrich:ClassEnrichmentResultSet](https://w3id.org/oak/class-enrichment/ClassEnrichmentResultSet) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ClassEnrichmentResult]0..\* - * Description: The enrichment results - * Range: [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/SortFieldEnum.md b/projects/class_enrichment/docs/SortFieldEnum.md deleted file mode 100644 index 227c37e4e..000000000 --- a/projects/class_enrichment/docs/SortFieldEnum.md +++ /dev/null @@ -1,21 +0,0 @@ - -# Enum: SortFieldEnum - - -The field to sort by - -URI: [ontoenrich:SortFieldEnum](https://w3id.org/oak/class-enrichment/SortFieldEnum) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| ANY | | | | -| P_VALUE | | | | - diff --git a/projects/class_enrichment/docs/classEnrichmentConfiguration__p_value_cutoff.md b/projects/class_enrichment/docs/classEnrichmentConfiguration__p_value_cutoff.md deleted file mode 100644 index a822f3cc1..000000000 --- a/projects/class_enrichment/docs/classEnrichmentConfiguration__p_value_cutoff.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: p_value_cutoff - - -p-value cutoff for enrichment - -URI: [ontoenrich:classEnrichmentConfiguration__p_value_cutoff](https://w3id.org/oak/class-enrichment/classEnrichmentConfiguration__p_value_cutoff) - - -## Domain and Range - -None → 1..1 [Float](types/Float.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentConfiguration](ClassEnrichmentConfiguration.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResultSet__results.md b/projects/class_enrichment/docs/classEnrichmentResultSet__results.md deleted file mode 100644 index 2425ab9dd..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResultSet__results.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: results - - -The enrichment results - -URI: [ontoenrich:classEnrichmentResultSet__results](https://w3id.org/oak/class-enrichment/classEnrichmentResultSet__results) - - -## Domain and Range - -None → 0..\* [ClassEnrichmentResult](ClassEnrichmentResult.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResultSet](ClassEnrichmentResultSet.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__ancestor_of_more_informative_result.md b/projects/class_enrichment/docs/classEnrichmentResult__ancestor_of_more_informative_result.md deleted file mode 100644 index 661700dbd..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__ancestor_of_more_informative_result.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: ancestor_of_more_informative_result - - -This term is more general than a previously reported result - -URI: [ontoenrich:classEnrichmentResult__ancestor_of_more_informative_result](https://w3id.org/oak/class-enrichment/classEnrichmentResult__ancestor_of_more_informative_result) - - -## Domain and Range - -None → 0..1 [Boolean](types/Boolean.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__background_count.md b/projects/class_enrichment/docs/classEnrichmentResult__background_count.md deleted file mode 100644 index 032ea8941..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__background_count.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: background_count - - -The background count - -URI: [ontoenrich:classEnrichmentResult__background_count](https://w3id.org/oak/class-enrichment/classEnrichmentResult__background_count) - - -## Domain and Range - -None → 0..1 [Integer](types/Integer.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__background_total.md b/projects/class_enrichment/docs/classEnrichmentResult__background_total.md deleted file mode 100644 index 3661ec524..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__background_total.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: background_total - - -The background total - -URI: [ontoenrich:classEnrichmentResult__background_total](https://w3id.org/oak/class-enrichment/classEnrichmentResult__background_total) - - -## Domain and Range - -None → 0..1 [Integer](types/Integer.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__class_id.md b/projects/class_enrichment/docs/classEnrichmentResult__class_id.md deleted file mode 100644 index 6c531b5a4..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__class_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: class_id - - -The class id - -URI: [ontoenrich:classEnrichmentResult__class_id](https://w3id.org/oak/class-enrichment/classEnrichmentResult__class_id) - - -## Domain and Range - -None → 1..1 [Uriorcurie](types/Uriorcurie.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__class_label.md b/projects/class_enrichment/docs/classEnrichmentResult__class_label.md deleted file mode 100644 index ae110d671..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__class_label.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: class_label - - -The class label - -URI: [ontoenrich:classEnrichmentResult__class_label](https://w3id.org/oak/class-enrichment/classEnrichmentResult__class_label) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__descendant_of_more_informative_result.md b/projects/class_enrichment/docs/classEnrichmentResult__descendant_of_more_informative_result.md deleted file mode 100644 index de7b17c3f..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__descendant_of_more_informative_result.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: descendant_of_more_informative_result - - -This term is more specific than a previously reported result - -URI: [ontoenrich:classEnrichmentResult__descendant_of_more_informative_result](https://w3id.org/oak/class-enrichment/classEnrichmentResult__descendant_of_more_informative_result) - - -## Domain and Range - -None → 0..1 [Boolean](types/Boolean.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__false_discovery_rate.md b/projects/class_enrichment/docs/classEnrichmentResult__false_discovery_rate.md deleted file mode 100644 index cee89a949..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__false_discovery_rate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: false_discovery_rate - - -The false discovery rate - -URI: [ontoenrich:classEnrichmentResult__false_discovery_rate](https://w3id.org/oak/class-enrichment/classEnrichmentResult__false_discovery_rate) - - -## Domain and Range - -None → 0..1 [Float](types/Float.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__fold_enrichment.md b/projects/class_enrichment/docs/classEnrichmentResult__fold_enrichment.md deleted file mode 100644 index 5f5042fa1..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__fold_enrichment.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: fold_enrichment - - -The fold enrichment - -URI: [ontoenrich:classEnrichmentResult__fold_enrichment](https://w3id.org/oak/class-enrichment/classEnrichmentResult__fold_enrichment) - - -## Domain and Range - -None → 0..1 [Float](types/Float.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__p_value.md b/projects/class_enrichment/docs/classEnrichmentResult__p_value.md deleted file mode 100644 index d96b4d544..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__p_value.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: p_value - - -The p-value - -URI: [ontoenrich:classEnrichmentResult__p_value](https://w3id.org/oak/class-enrichment/classEnrichmentResult__p_value) - - -## Domain and Range - -None → 1..1 [Float](types/Float.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | OBI:0000175 | - diff --git a/projects/class_enrichment/docs/classEnrichmentResult__p_value_adjusted.md b/projects/class_enrichment/docs/classEnrichmentResult__p_value_adjusted.md deleted file mode 100644 index 26e3efb03..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__p_value_adjusted.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: p_value_adjusted - - -The adjusted p-value - -URI: [ontoenrich:classEnrichmentResult__p_value_adjusted](https://w3id.org/oak/class-enrichment/classEnrichmentResult__p_value_adjusted) - - -## Domain and Range - -None → 0..1 [Float](types/Float.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__probability.md b/projects/class_enrichment/docs/classEnrichmentResult__probability.md deleted file mode 100644 index 51e5d9f30..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__probability.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: probability - - -The probability, as estimated by model-based approaches - -URI: [ontoenrich:classEnrichmentResult__probability](https://w3id.org/oak/class-enrichment/classEnrichmentResult__probability) - - -## Domain and Range - -None → 0..1 [Float](types/Float.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__rank.md b/projects/class_enrichment/docs/classEnrichmentResult__rank.md deleted file mode 100644 index c129300ea..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__rank.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: rank - - -The rank of this result - -URI: [ontoenrich:classEnrichmentResult__rank](https://w3id.org/oak/class-enrichment/classEnrichmentResult__rank) - - -## Domain and Range - -None → 0..1 [Integer](types/Integer.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__sample_count.md b/projects/class_enrichment/docs/classEnrichmentResult__sample_count.md deleted file mode 100644 index 0ff4e269f..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__sample_count.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: sample_count - - -The number of entities in the sample with this class - -URI: [ontoenrich:classEnrichmentResult__sample_count](https://w3id.org/oak/class-enrichment/classEnrichmentResult__sample_count) - - -## Domain and Range - -None → 0..1 [Integer](types/Integer.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/classEnrichmentResult__sample_total.md b/projects/class_enrichment/docs/classEnrichmentResult__sample_total.md deleted file mode 100644 index 51f263d7b..000000000 --- a/projects/class_enrichment/docs/classEnrichmentResult__sample_total.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: sample_total - - -The total number of entities in the sample - -URI: [ontoenrich:classEnrichmentResult__sample_total](https://w3id.org/oak/class-enrichment/classEnrichmentResult__sample_total) - - -## Domain and Range - -None → 0..1 [Integer](types/Integer.md) - -## Parents - - -## Children - - -## Used by - - * [ClassEnrichmentResult](ClassEnrichmentResult.md) diff --git a/projects/class_enrichment/docs/class_enrichment.md b/projects/class_enrichment/docs/class_enrichment.md deleted file mode 100644 index e2cc53aa3..000000000 --- a/projects/class_enrichment/docs/class_enrichment.md +++ /dev/null @@ -1,89 +0,0 @@ - -# class-enrichment - - -**metamodel version:** 1.7.0 - -**version:** None - - -A datamodel for representing the results of class enrichment on gene sets - - -### Classes - - * [ClassEnrichmentConfiguration](ClassEnrichmentConfiguration.md) - configuration for search - * [ClassEnrichmentResult](ClassEnrichmentResult.md) - A single enrichment result - * [ClassEnrichmentResultSet](ClassEnrichmentResultSet.md) - A collection of enrichemt results - -### Mixins - - -### Slots - - * [➞p_value_cutoff](classEnrichmentConfiguration__p_value_cutoff.md) - p-value cutoff for enrichment - * [➞results](classEnrichmentResultSet__results.md) - The enrichment results - * [➞ancestor_of_more_informative_result](classEnrichmentResult__ancestor_of_more_informative_result.md) - This term is more general than a previously reported result - * [➞background_count](classEnrichmentResult__background_count.md) - The background count - * [➞background_total](classEnrichmentResult__background_total.md) - The background total - * [➞class_id](classEnrichmentResult__class_id.md) - The class id - * [➞class_label](classEnrichmentResult__class_label.md) - The class label - * [➞descendant_of_more_informative_result](classEnrichmentResult__descendant_of_more_informative_result.md) - This term is more specific than a previously reported result - * [➞false_discovery_rate](classEnrichmentResult__false_discovery_rate.md) - The false discovery rate - * [➞fold_enrichment](classEnrichmentResult__fold_enrichment.md) - The fold enrichment - * [➞p_value](classEnrichmentResult__p_value.md) - The p-value - * [➞p_value_adjusted](classEnrichmentResult__p_value_adjusted.md) - The adjusted p-value - * [➞probability](classEnrichmentResult__probability.md) - The probability, as estimated by model-based approaches - * [➞rank](classEnrichmentResult__rank.md) - The rank of this result - * [➞sample_count](classEnrichmentResult__sample_count.md) - The number of entities in the sample with this class - * [➞sample_total](classEnrichmentResult__sample_total.md) - The total number of entities in the sample - -### Enums - - * [SortFieldEnum](SortFieldEnum.md) - The field to sort by - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Position](types/Position.md) ([Integer](types/Integer.md)) - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/class_enrichment/docs/types/Boolean.md b/projects/class_enrichment/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/class_enrichment/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/class_enrichment/docs/types/Curie.md b/projects/class_enrichment/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/class_enrichment/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/class_enrichment/docs/types/Date.md b/projects/class_enrichment/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/class_enrichment/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/class_enrichment/docs/types/DateOrDatetime.md b/projects/class_enrichment/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/class_enrichment/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/class_enrichment/docs/types/Datetime.md b/projects/class_enrichment/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/class_enrichment/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/class_enrichment/docs/types/Decimal.md b/projects/class_enrichment/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/class_enrichment/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/class_enrichment/docs/types/Double.md b/projects/class_enrichment/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/class_enrichment/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/class_enrichment/docs/types/Float.md b/projects/class_enrichment/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/class_enrichment/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/class_enrichment/docs/types/Integer.md b/projects/class_enrichment/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/class_enrichment/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/class_enrichment/docs/types/Jsonpath.md b/projects/class_enrichment/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/class_enrichment/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/class_enrichment/docs/types/Jsonpointer.md b/projects/class_enrichment/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/class_enrichment/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/class_enrichment/docs/types/Ncname.md b/projects/class_enrichment/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/class_enrichment/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/class_enrichment/docs/types/Nodeidentifier.md b/projects/class_enrichment/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/class_enrichment/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/class_enrichment/docs/types/Objectidentifier.md b/projects/class_enrichment/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/class_enrichment/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/class_enrichment/docs/types/Position.md b/projects/class_enrichment/docs/types/Position.md deleted file mode 100644 index ad3e7e98d..000000000 --- a/projects/class_enrichment/docs/types/Position.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: Position - - - - -URI: [ontoenrich:Position](https://w3id.org/oak/class-enrichment/Position) - -| | | | -| --- | --- | --- | -| Parent type | | [Integer](types/Integer.md) | -| Root (builtin) type | | **int** | diff --git a/projects/class_enrichment/docs/types/Sparqlpath.md b/projects/class_enrichment/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/class_enrichment/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/class_enrichment/docs/types/String.md b/projects/class_enrichment/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/class_enrichment/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/class_enrichment/docs/types/Time.md b/projects/class_enrichment/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/class_enrichment/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/class_enrichment/docs/types/Uri.md b/projects/class_enrichment/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/class_enrichment/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or 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z-Y+Zw;D`41@96(*`mV#TFTZ}nhfqKN538{21lJ#a{!8Fbg8P%;A0LITvs|C#f3t+4 z<_T07*I9nf_19UhkEg#`PVoPc<>#<^o#px@^IsM;3e;eOiskoQa~*oU5&ee7qRRE( z+R}C4^}_xe=z&@=|NsC0Pno|CzFvragR#kfg8!u~UFW%;-oJT{Q9S>U>{{wrsJ-cr Qo=X7eNA=#jKTHkyKUb;}r2qf` diff --git a/projects/class_enrichment/graphql/class_enrichment.graphql b/projects/class_enrichment/graphql/class_enrichment.graphql deleted file mode 100644 index d554fb474..000000000 --- a/projects/class_enrichment/graphql/class_enrichment.graphql +++ /dev/null @@ -1,28 +0,0 @@ -type ClassEnrichmentConfiguration - { - pValueCutoff: Float! - } - -type ClassEnrichmentResult - { - classId: Uriorcurie! - classLabel: String - rank: Integer - pValue: Float! - pValueAdjusted: Float - falseDiscoveryRate: Float - foldEnrichment: Float - probability: Float - sampleCount: Integer - sampleTotal: Integer - backgroundCount: Integer - backgroundTotal: Integer - ancestorOfMoreInformativeResult: Boolean - descendantOfMoreInformativeResult: Boolean - } - -type ClassEnrichmentResultSet - { - results: [ClassEnrichmentResult] - } - diff --git a/projects/class_enrichment/jsonld/class_enrichment.context.jsonld b/projects/class_enrichment/jsonld/class_enrichment.context.jsonld deleted file mode 100644 index 4ebfa58fc..000000000 --- a/projects/class_enrichment/jsonld/class_enrichment.context.jsonld +++ /dev/null @@ -1,78 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:51:40", - "source": "class_enrichment.yaml" - }, - "@context": { - "OBI": { - "@id": "http://purl.obolibrary.org/obo/OBI_", - "@prefix": true - }, - "STATO": { - "@id": "http://purl.obolibrary.org/obo/STATO_", - "@prefix": true - }, - "bpa": "https://bioportal.bioontology.org/annotator/", - "linkml": "https://w3id.org/linkml/", - "oa": "http://www.w3.org/ns/oa#", - "ontoenrich": "https://w3id.org/oak/class-enrichment/", - "owl": "http://www.w3.org/2002/07/owl#", - "pav": "http://purl.org/pav/", - "prov": "http://www.w3.org/ns/prov#", - "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "schema": "http://schema.org/", - "sh": "https://w3id.org/shacl/", - "skos": "http://www.w3.org/2004/02/skos/core#", - "sssom": "http://w3id.org/sssom/", - "xsd": "http://www.w3.org/2001/XMLSchema#", - "@vocab": "https://w3id.org/oak/class-enrichment/", - "p_value_cutoff": { - "@type": "xsd:float" - }, - "ancestor_of_more_informative_result": { - "@type": "xsd:boolean" - }, - "background_count": { - "@type": "xsd:integer" - }, - "background_total": { - "@type": "xsd:integer" - }, - "class_id": { - "@type": "@id" - }, - "descendant_of_more_informative_result": { - "@type": "xsd:boolean" - }, - "false_discovery_rate": { - "@type": "xsd:float" - }, - "fold_enrichment": { - "@type": "xsd:float" - }, - "p_value": { - "@type": "xsd:float", - "@id": "OBI:0000175" - }, - "p_value_adjusted": { - "@type": "xsd:float" - }, - "probability": { - "@type": "xsd:float" - }, - "rank": { - "@type": "xsd:integer" - }, - "sample_count": { - "@type": "xsd:integer" - }, - "sample_total": { - "@type": "xsd:integer" - }, - "results": { - "@type": "@id" - } - } -} diff --git a/projects/class_enrichment/jsonld/class_enrichment.jsonld b/projects/class_enrichment/jsonld/class_enrichment.jsonld deleted file mode 100644 index 763a76a58..000000000 --- a/projects/class_enrichment/jsonld/class_enrichment.jsonld +++ /dev/null @@ -1,747 +0,0 @@ -{ - "name": "class-enrichment", - "description": "A datamodel for representing the results of class enrichment on gene sets", - "title": "Class Enrichment Datamodel", - "id": "https://w3id.org/oak/class-enrichment", - "imports": [ - "linkml:types" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "ontoenrich", - "prefix_reference": "https://w3id.org/oak/class-enrichment/" - }, - { - "prefix_prefix": "skos", - "prefix_reference": "http://www.w3.org/2004/02/skos/core#" - }, - { - "prefix_prefix": "pav", - "prefix_reference": "http://purl.org/pav/" - }, - { - "prefix_prefix": "schema", - "prefix_reference": "http://schema.org/" - }, - { - "prefix_prefix": "sh", - "prefix_reference": "https://w3id.org/shacl/" - }, - { - "prefix_prefix": "prov", - "prefix_reference": "http://www.w3.org/ns/prov#" - }, - { - "prefix_prefix": "sssom", - "prefix_reference": "http://w3id.org/sssom/" - }, - { - "prefix_prefix": "bpa", - "prefix_reference": "https://bioportal.bioontology.org/annotator/" - }, - { - "prefix_prefix": "oa", - "prefix_reference": "http://www.w3.org/ns/oa#" - }, - { - "prefix_prefix": "STATO", - "prefix_reference": "http://purl.obolibrary.org/obo/STATO_" - }, - { - "prefix_prefix": "OBI", - "prefix_reference": "http://purl.obolibrary.org/obo/OBI_" - } - ], - "emit_prefixes": [ - "linkml", - "rdf", - "rdfs", - "xsd", - "owl" - ], - "default_curi_maps": [ - "semweb_context" - ], - "default_prefix": "ontoenrich", - "default_range": "string", - "types": [ - { - "name": "Position", - "definition_uri": "https://w3id.org/oak/class-enrichment/Position", - "from_schema": "https://w3id.org/oak/class-enrichment", - "typeof": "integer", - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "SortFieldEnum", - "definition_uri": "https://w3id.org/oak/class-enrichment/SortFieldEnum", - "description": "The field to sort by", - "from_schema": "https://w3id.org/oak/class-enrichment", - "permissible_values": [ - { - "text": "ANY" - }, - { - "text": "P_VALUE" - } - ] - } - ], - "slots": [ - { - "name": "classEnrichmentConfiguration__p_value_cutoff", - "description": "p-value cutoff for enrichment", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/p_value_cutoff", - "alias": "p_value_cutoff", - "owner": "ClassEnrichmentConfiguration", - "domain_of": [ - "ClassEnrichmentConfiguration" - ], - "range": "float", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResultSet__results", - "description": "The enrichment results", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/results", - "multivalued": true, - "alias": "results", - "owner": "ClassEnrichmentResultSet", - "domain_of": [ - "ClassEnrichmentResultSet" - ], - "range": "ClassEnrichmentResult", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__class_id", - "description": "The class id", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/class_id", - "alias": "class_id", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "uriorcurie", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__class_label", - "description": "The class label", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/class_label", - "alias": "class_label", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__rank", - "description": "The rank of this result", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/rank", - "alias": "rank", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__p_value", - "description": "The p-value", - "from_schema": "https://w3id.org/oak/class-enrichment", - "mappings": [ - "http://purl.obolibrary.org/obo/OBI_0000175" - ], - "slot_uri": "http://purl.obolibrary.org/obo/OBI_0000175", - "alias": "p_value", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "float", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__p_value_adjusted", - "description": "The adjusted p-value", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/p_value_adjusted", - "alias": "p_value_adjusted", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "float", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__false_discovery_rate", - "description": "The false discovery rate", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/false_discovery_rate", - "alias": "false_discovery_rate", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "float", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__fold_enrichment", - "description": "The fold enrichment", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/fold_enrichment", - "alias": "fold_enrichment", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "float", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__probability", - "description": "The probability, as estimated by model-based approaches", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/probability", - "alias": "probability", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "float", - "minimum_value": 0, - "maximum_value": 1, - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__sample_count", - "description": "The number of entities in the sample with this class", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/sample_count", - "alias": "sample_count", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__sample_total", - "description": "The total number of entities in the sample", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/sample_total", - "alias": "sample_total", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__background_count", - "description": "The background count", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/background_count", - "alias": "background_count", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__background_total", - "description": "The background total", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/background_total", - "alias": "background_total", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__ancestor_of_more_informative_result", - "description": "This term is more general than a previously reported result", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/ancestor_of_more_informative_result", - "alias": "ancestor_of_more_informative_result", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "boolean", - "@type": "SlotDefinition" - }, - { - "name": "classEnrichmentResult__descendant_of_more_informative_result", - "description": "This term is more specific than a previously reported result", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slot_uri": "https://w3id.org/oak/class-enrichment/descendant_of_more_informative_result", - "alias": "descendant_of_more_informative_result", - "owner": "ClassEnrichmentResult", - "domain_of": [ - "ClassEnrichmentResult" - ], - "range": "boolean", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "ClassEnrichmentConfiguration", - "definition_uri": "https://w3id.org/oak/class-enrichment/ClassEnrichmentConfiguration", - "description": "configuration for search", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slots": [ - "classEnrichmentConfiguration__p_value_cutoff" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "p_value_cutoff", - "description": "p-value cutoff for enrichment", - "range": "float", - "required": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "https://w3id.org/oak/class-enrichment/ClassEnrichmentConfiguration", - "@type": "ClassDefinition" - }, - { - "name": "ClassEnrichmentResultSet", - "definition_uri": "https://w3id.org/oak/class-enrichment/ClassEnrichmentResultSet", - "description": "A collection of enrichemt results", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slots": [ - "classEnrichmentResultSet__results" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "results", - "description": "The enrichment results", - "multivalued": true, - "range": "ClassEnrichmentResult", - "@type": "SlotDefinition" - } - ], - "class_uri": "https://w3id.org/oak/class-enrichment/ClassEnrichmentResultSet", - "@type": "ClassDefinition" - }, - { - "name": "ClassEnrichmentResult", - "definition_uri": "https://w3id.org/oak/class-enrichment/ClassEnrichmentResult", - "description": "A single enrichment result", - "from_schema": "https://w3id.org/oak/class-enrichment", - "slots": [ - "classEnrichmentResult__class_id", - "classEnrichmentResult__class_label", - "classEnrichmentResult__rank", - "classEnrichmentResult__p_value", - "classEnrichmentResult__p_value_adjusted", - "classEnrichmentResult__false_discovery_rate", - "classEnrichmentResult__fold_enrichment", - "classEnrichmentResult__probability", - "classEnrichmentResult__sample_count", - "classEnrichmentResult__sample_total", - "classEnrichmentResult__background_count", - "classEnrichmentResult__background_total", - "classEnrichmentResult__ancestor_of_more_informative_result", - "classEnrichmentResult__descendant_of_more_informative_result" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "class_id", - "description": "The class id", - "range": "uriorcurie", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "class_label", - "description": "The class label", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "rank", - "description": "The rank of this result", - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "p_value", - "description": "The p-value", - "slot_uri": "OBI:0000175", - "range": "float", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "p_value_adjusted", - "description": "The adjusted p-value", - "range": "float", - "@type": "SlotDefinition" - }, - { - "name": "false_discovery_rate", - "description": "The false discovery rate", - "range": "float", - "@type": "SlotDefinition" - }, - { - "name": "fold_enrichment", - "description": "The fold enrichment", - "range": "float", - "@type": "SlotDefinition" - }, - { - "name": "probability", - "description": "The probability, as estimated by model-based approaches", - "range": "float", - "minimum_value": 0, - "maximum_value": 1, - "@type": "SlotDefinition" - }, - { - "name": "sample_count", - "description": "The number of entities in the sample with this class", - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "sample_total", - "description": "The total number of entities in the sample", - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "background_count", - "description": "The background count", - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "background_total", - "description": "The background total", - "range": "integer", - "@type": "SlotDefinition" - }, - { - "name": "ancestor_of_more_informative_result", - "description": "This term is more general than a previously reported result", - "range": "boolean", - "@type": "SlotDefinition" - }, - { - "name": "descendant_of_more_informative_result", - "description": "This term is more specific than a previously reported result", - "range": "boolean", - "@type": "SlotDefinition" - } - ], - "class_uri": "https://w3id.org/oak/class-enrichment/ClassEnrichmentResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "class_enrichment.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 3192, - "generation_date": "2023-08-07T10:51:41", - "@type": "SchemaDefinition", - "@context": [ - "projects/class_enrichment/jsonld/class_enrichment.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - { - "@base": "https://w3id.org/oak/class-enrichment/" - } - ] -} diff --git a/projects/class_enrichment/jsonschema/class_enrichment.schema.json b/projects/class_enrichment/jsonschema/class_enrichment.schema.json deleted file mode 100644 index 4a0c9036d..000000000 --- a/projects/class_enrichment/jsonschema/class_enrichment.schema.json +++ /dev/null @@ -1,120 +0,0 @@ -{ - "$defs": { - "ClassEnrichmentConfiguration": { - "additionalProperties": false, - "description": "configuration for search", - "properties": { - "p_value_cutoff": { - "description": "p-value cutoff for enrichment", - "type": "number" - } - }, - "required": [ - "p_value_cutoff" - ], - "title": "ClassEnrichmentConfiguration", - "type": "object" - }, - "ClassEnrichmentResult": { - "additionalProperties": false, - "description": "A single enrichment result", - "properties": { - "ancestor_of_more_informative_result": { - "description": "This term is more general than a previously reported result", - "type": "boolean" - }, - "background_count": { - "description": "The background count", - "type": "integer" - }, - "background_total": { - "description": "The background total", - "type": "integer" - }, - "class_id": { - "description": "The class id", - "type": "string" - }, - "class_label": { - "description": "The class label", - "type": "string" - }, - "descendant_of_more_informative_result": { - "description": "This term is more specific than a previously reported result", - "type": "boolean" - }, - "false_discovery_rate": { - "description": "The false discovery rate", - "type": "number" - }, - "fold_enrichment": { - "description": "The fold enrichment", - "type": "number" - }, - "p_value": { - "description": "The p-value", - "type": "number" - }, - "p_value_adjusted": { - "description": "The adjusted p-value", - "type": "number" - }, - "probability": { - "description": "The probability, as estimated by model-based approaches", - "maximum": 1, - "minimum": 0, - "type": "number" - }, - "rank": { - "description": "The rank of this result", - "type": "integer" - }, - "sample_count": { - "description": "The number of entities in the sample with this class", - "type": "integer" - }, - "sample_total": { - "description": "The total number of entities in the sample", - "type": "integer" - } - }, - "required": [ - "class_id", - "p_value" - ], - "title": "ClassEnrichmentResult", - "type": "object" - }, - "ClassEnrichmentResultSet": { - "additionalProperties": false, - "description": "A collection of enrichemt results", - "properties": { - "results": { - "description": "The enrichment results", - "items": { - "$ref": "#/$defs/ClassEnrichmentResult" - }, - "type": "array" - } - }, - "title": "ClassEnrichmentResultSet", - "type": "object" - }, - "SortFieldEnum": { - "description": "The field to sort by", - "enum": [ - "ANY", - "P_VALUE" - ], - "title": "SortFieldEnum", - "type": "string" - } - }, - "$id": "https://w3id.org/oak/class-enrichment", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "class-enrichment", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/class_enrichment/owl/class_enrichment.owl.ttl b/projects/class_enrichment/owl/class_enrichment.owl.ttl deleted file mode 100644 index 0575e121d..000000000 --- a/projects/class_enrichment/owl/class_enrichment.owl.ttl +++ /dev/null @@ -1,246 +0,0 @@ -@prefix IAO: . -@prefix OBI: . -@prefix linkml: . -@prefix ontoenrich: . -@prefix owl: . -@prefix rdf: . -@prefix rdfs: . -@prefix skos: . -@prefix xsd: . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - - a owl:Ontology ; - rdfs:label "class-enrichment" ; - IAO:0000700 ontoenrich:ClassEnrichmentConfiguration, - ontoenrich:ClassEnrichmentResult, - ontoenrich:ClassEnrichmentResultSet ; - linkml:classes "{'ClassEnrichmentConfiguration': ClassDefinition(name='ClassEnrichmentConfiguration', id_prefixes=[], definition_uri='https://w3id.org/oak/class-enrichment/ClassEnrichmentConfiguration', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='configuration for search', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/oak/class-enrichment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['classEnrichmentConfiguration__p_value_cutoff'], slot_usage={}, attributes={'p_value_cutoff': SlotDefinition(name='p_value_cutoff', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='p-value cutoff for enrichment', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='ontoenrich:ClassEnrichmentConfiguration', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ClassEnrichmentResultSet': ClassDefinition(name='ClassEnrichmentResultSet', id_prefixes=[], definition_uri='https://w3id.org/oak/class-enrichment/ClassEnrichmentResultSet', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A collection of enrichemt results', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/oak/class-enrichment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['classEnrichmentResultSet__results'], slot_usage={}, attributes={'results': SlotDefinition(name='results', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The enrichment results', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ClassEnrichmentResult', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='ontoenrich:ClassEnrichmentResultSet', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ClassEnrichmentResult': ClassDefinition(name='ClassEnrichmentResult', id_prefixes=[], definition_uri='https://w3id.org/oak/class-enrichment/ClassEnrichmentResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A single enrichment result', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/oak/class-enrichment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['classEnrichmentResult__class_id', 'classEnrichmentResult__class_label', 'classEnrichmentResult__rank', 'classEnrichmentResult__p_value', 'classEnrichmentResult__p_value_adjusted', 'classEnrichmentResult__false_discovery_rate', 'classEnrichmentResult__fold_enrichment', 'classEnrichmentResult__probability', 'classEnrichmentResult__sample_count', 'classEnrichmentResult__sample_total', 'classEnrichmentResult__background_count', 'classEnrichmentResult__background_total', 'classEnrichmentResult__ancestor_of_more_informative_result', 'classEnrichmentResult__descendant_of_more_informative_result'], slot_usage={}, attributes={'class_id': SlotDefinition(name='class_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The class id', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='uriorcurie', range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'class_label': SlotDefinition(name='class_label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The class label', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'rank': SlotDefinition(name='rank', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The rank of this result', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'p_value': SlotDefinition(name='p_value', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The p-value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='OBI:0000175', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'p_value_adjusted': SlotDefinition(name='p_value_adjusted', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The adjusted p-value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'false_discovery_rate': SlotDefinition(name='false_discovery_rate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The false discovery rate', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'fold_enrichment': SlotDefinition(name='fold_enrichment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The fold enrichment', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'probability': SlotDefinition(name='probability', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The probability, as estimated by model-based approaches', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=0, maximum_value=1, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sample_count': SlotDefinition(name='sample_count', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The number of entities in the sample with this class', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sample_total': SlotDefinition(name='sample_total', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The total number of entities in the sample', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'background_count': SlotDefinition(name='background_count', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The background count', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'background_total': SlotDefinition(name='background_total', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The background total', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ancestor_of_more_informative_result': SlotDefinition(name='ancestor_of_more_informative_result', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='This term is more general than a previously reported result', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='boolean', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'descendant_of_more_informative_result': SlotDefinition(name='descendant_of_more_informative_result', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='This term is more specific than a previously reported result', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='boolean', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='ontoenrich:ClassEnrichmentResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'SortFieldEnum': EnumDefinition(name='SortFieldEnum', id_prefixes=[], definition_uri='https://w3id.org/oak/class-enrichment/SortFieldEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The field to sort by', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/oak/class-enrichment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'ANY': PermissibleValue(text='ANY', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'P_VALUE': PermissibleValue(text='P_VALUE', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/oak/class-enrichment" ; - linkml:imports "linkml:types" ; - linkml:types "{'Position': TypeDefinition(name='Position', id_prefixes=[], definition_uri='https://w3id.org/oak/class-enrichment/Position', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/oak/class-enrichment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof='integer', base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -ontoenrich:Position a owl:Class, - linkml:TypeDefinition ; - rdfs:label "Position" ; - rdfs:subClassOf linkml:Integer . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -ontoenrich:ClassEnrichmentConfiguration a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ClassEnrichmentConfiguration" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Float ; - owl:onProperty ontoenrich:p_value_cutoff ; - owl:qualifiedCardinality 1 ] ; - skos:definition "configuration for search" ; - linkml:attributes "{'p_value_cutoff': SlotDefinition(name='p_value_cutoff', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='p-value cutoff for enrichment', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -ontoenrich:ClassEnrichmentResultSet a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ClassEnrichmentResultSet" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ontoenrich:ClassEnrichmentResult ; - owl:onProperty ontoenrich:results ] ; - skos:definition "A collection of enrichemt results" ; - linkml:attributes "{'results': SlotDefinition(name='results', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The enrichment results', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ClassEnrichmentResult', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -ontoenrich:ancestor_of_more_informative_result a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ancestor_of_more_informative_result" ; - rdfs:range linkml:Boolean ; - skos:definition "This term is more general than a previously reported result" . - -ontoenrich:background_count a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "background_count" ; - rdfs:range linkml:Integer ; - skos:definition "The background count" . - -ontoenrich:background_total a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "background_total" ; - rdfs:range linkml:Integer ; - skos:definition "The background total" . - -ontoenrich:class_id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "class_id" ; - rdfs:range linkml:Uriorcurie ; - skos:definition "The class id" . - -ontoenrich:class_label a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "class_label" ; - rdfs:range linkml:String ; - skos:definition "The class label" . - -ontoenrich:descendant_of_more_informative_result a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "descendant_of_more_informative_result" ; - rdfs:range linkml:Boolean ; - skos:definition "This term is more specific than a previously reported result" . - -ontoenrich:false_discovery_rate a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "false_discovery_rate" ; - rdfs:range linkml:Float ; - skos:definition "The false discovery rate" . - -ontoenrich:fold_enrichment a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "fold_enrichment" ; - rdfs:range linkml:Float ; - skos:definition "The fold enrichment" . - -ontoenrich:p_value_adjusted a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "p_value_adjusted" ; - rdfs:range linkml:Float ; - skos:definition "The adjusted p-value" . - -ontoenrich:p_value_cutoff a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "p_value_cutoff" ; - rdfs:range linkml:Float ; - skos:definition "p-value cutoff for enrichment" . - -ontoenrich:probability a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "probability" ; - rdfs:range linkml:Float ; - skos:definition "The probability, as estimated by model-based approaches" . - -ontoenrich:rank a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "rank" ; - rdfs:range linkml:Integer ; - skos:definition "The rank of this result" . - -ontoenrich:results a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "results" ; - rdfs:range ontoenrich:ClassEnrichmentResult ; - skos:definition "The enrichment results" . - -ontoenrich:sample_count a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "sample_count" ; - rdfs:range linkml:Integer ; - skos:definition "The number of entities in the sample with this class" . - -ontoenrich:sample_total a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "sample_total" ; - rdfs:range linkml:Integer ; - skos:definition "The total number of entities in the sample" . - -OBI:0000175 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "p_value" ; - rdfs:range linkml:Float ; - skos:definition "The p-value" ; - skos:exactMatch OBI:0000175 . - -ontoenrich:SortFieldEnum a owl:Class, - linkml:EnumDefinition ; - rdfs:label "SortFieldEnum" ; - owl:unionOf ( ) ; - linkml:permissible_values , - . - - a owl:Class, - ontoenrich:SortFieldEnum ; - rdfs:label "ANY" . - - a owl:Class, - ontoenrich:SortFieldEnum ; - rdfs:label "P_VALUE" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -ontoenrich:ClassEnrichmentResult a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ClassEnrichmentResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty ontoenrich:background_count ], - [ a owl:Restriction ; - owl:onClass linkml:Float ; - owl:onProperty OBI:0000175 ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty ontoenrich:p_value_adjusted ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty ontoenrich:ancestor_of_more_informative_result ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty ontoenrich:false_discovery_rate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ontoenrich:class_label ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty ontoenrich:sample_total ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty ontoenrich:rank ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty ontoenrich:class_id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty ontoenrich:probability ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty ontoenrich:sample_count ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Float ; - owl:onProperty ontoenrich:fold_enrichment ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty ontoenrich:background_total ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty ontoenrich:descendant_of_more_informative_result ] ; - skos:definition "A single enrichment result" ; - linkml:attributes "{'class_id': SlotDefinition(name='class_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The class id', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='uriorcurie', range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'class_label': SlotDefinition(name='class_label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The class label', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'rank': SlotDefinition(name='rank', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The rank of this result', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'p_value': SlotDefinition(name='p_value', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The p-value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='OBI:0000175', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'p_value_adjusted': SlotDefinition(name='p_value_adjusted', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The adjusted p-value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'false_discovery_rate': SlotDefinition(name='false_discovery_rate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The false discovery rate', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'fold_enrichment': SlotDefinition(name='fold_enrichment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The fold enrichment', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'probability': SlotDefinition(name='probability', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The probability, as estimated by model-based approaches', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='float', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=0, maximum_value=1, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sample_count': SlotDefinition(name='sample_count', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The number of entities in the sample with this class', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sample_total': SlotDefinition(name='sample_total', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The total number of entities in the sample', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'background_count': SlotDefinition(name='background_count', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The background count', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'background_total': SlotDefinition(name='background_total', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The background total', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='integer', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ancestor_of_more_informative_result': SlotDefinition(name='ancestor_of_more_informative_result', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='This term is more general than a previously reported result', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='boolean', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'descendant_of_more_informative_result': SlotDefinition(name='descendant_of_more_informative_result', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='This term is more specific than a previously reported result', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='boolean', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/class_enrichment/prefixmap/class_enrichment.yaml b/projects/class_enrichment/prefixmap/class_enrichment.yaml deleted file mode 100644 index a598bd14d..000000000 --- a/projects/class_enrichment/prefixmap/class_enrichment.yaml +++ /dev/null @@ -1,18 +0,0 @@ -{ - "OBI": "http://purl.obolibrary.org/obo/OBI_", - "STATO": "http://purl.obolibrary.org/obo/STATO_", - "bpa": "https://bioportal.bioontology.org/annotator/", - "linkml": "https://w3id.org/linkml/", - "oa": "http://www.w3.org/ns/oa#", - "ontoenrich": "https://w3id.org/oak/class-enrichment/", - "owl": "http://www.w3.org/2002/07/owl#", - "pav": "http://purl.org/pav/", - "prov": "http://www.w3.org/ns/prov#", - "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", - "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "schema": "http://schema.org/", - "sh": "https://w3id.org/shacl/", - "skos": "http://www.w3.org/2004/02/skos/core#", - "sssom": "http://w3id.org/sssom/", - "xsd": "http://www.w3.org/2001/XMLSchema#" -} diff --git a/projects/class_enrichment/protobuf/class_enrichment.proto b/projects/class_enrichment/protobuf/class_enrichment.proto deleted file mode 100644 index 8079fd0cf..000000000 --- a/projects/class_enrichment/protobuf/class_enrichment.proto +++ /dev/null @@ -1,28 +0,0 @@ -// configuration for search -message ClassEnrichmentConfiguration - { - float pValueCutoff = 0 - } -// A single enrichment result -message ClassEnrichmentResult - { - uriorcurie classId = 0 - string classLabel = 0 - integer rank = 0 - float pValue = 0 - float pValueAdjusted = 0 - float falseDiscoveryRate = 0 - float foldEnrichment = 0 - float probability = 0 - integer sampleCount = 0 - integer sampleTotal = 0 - integer backgroundCount = 0 - integer backgroundTotal = 0 - boolean ancestorOfMoreInformativeResult = 0 - boolean descendantOfMoreInformativeResult = 0 - } -// A collection of enrichemt results -message ClassEnrichmentResultSet - { - repeated classEnrichmentResult results = 0 - } diff --git a/projects/class_enrichment/shacl/class_enrichment.shacl.ttl b/projects/class_enrichment/shacl/class_enrichment.shacl.ttl deleted file mode 100644 index 73c339319..000000000 --- a/projects/class_enrichment/shacl/class_enrichment.shacl.ttl +++ /dev/null @@ -1,94 +0,0 @@ -@prefix OBI: . -@prefix ontoenrich: . -@prefix rdf: . -@prefix sh: . -@prefix xsd: . - -ontoenrich:ClassEnrichmentConfiguration a sh:NodeShape ; - sh:closed true ; - sh:description "configuration for search" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "p-value cutoff for enrichment" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ontoenrich:p_value_cutoff ] ; - sh:targetClass ontoenrich:ClassEnrichmentConfiguration . - -ontoenrich:ClassEnrichmentResultSet a sh:NodeShape ; - sh:closed true ; - sh:description "A collection of enrichemt results" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ontoenrich:ClassEnrichmentResult ; - sh:description "The enrichment results" ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path ontoenrich:results ] ; - sh:targetClass ontoenrich:ClassEnrichmentResultSet . - -ontoenrich:ClassEnrichmentResult a sh:NodeShape ; - sh:closed true ; - sh:description "A single enrichment result" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The rank of this result" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path ontoenrich:rank ], - [ sh:description "The probability, as estimated by model-based approaches" ; - sh:maxCount 1 ; - sh:maxInclusive 1 ; - sh:minInclusive 0 ; - sh:order 7 ; - sh:path ontoenrich:probability ], - [ sh:description "The class label" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ontoenrich:class_label ], - [ sh:description "The adjusted p-value" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path ontoenrich:p_value_adjusted ], - [ sh:description "The background total" ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path ontoenrich:background_total ], - [ sh:description "The number of entities in the sample with this class" ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path ontoenrich:sample_count ], - [ sh:description "This term is more specific than a previously reported result" ; - sh:maxCount 1 ; - sh:order 13 ; - sh:path ontoenrich:descendant_of_more_informative_result ], - [ sh:description "The class id" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ontoenrich:class_id ], - [ sh:description "This term is more general than a previously reported result" ; - sh:maxCount 1 ; - sh:order 12 ; - sh:path ontoenrich:ancestor_of_more_informative_result ], - [ sh:description "The fold enrichment" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path ontoenrich:fold_enrichment ], - [ sh:description "The total number of entities in the sample" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path ontoenrich:sample_total ], - [ sh:description "The background count" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path ontoenrich:background_count ], - [ sh:description "The false discovery rate" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path ontoenrich:false_discovery_rate ], - [ sh:description "The p-value" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path OBI:0000175 ] ; - sh:targetClass ontoenrich:ClassEnrichmentResult . - diff --git a/projects/class_enrichment/shex/class_enrichment.shex b/projects/class_enrichment/shex/class_enrichment.shex deleted file mode 100644 index b18547db1..000000000 --- a/projects/class_enrichment/shex/class_enrichment.shex +++ /dev/null @@ -1,79 +0,0 @@ -BASE -PREFIX rdf: -PREFIX xsd: -PREFIX linkml: - - - xsd:integer - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - - CLOSED { - ( $ @linkml:Float ; - rdf:type [ ] ? - ) -} - - CLOSED { - ( $ ( @linkml:Uriorcurie ; - @linkml:String ? ; - @linkml:Integer ? ; - @linkml:Float ; - @linkml:Float ? ; - @linkml:Float ? ; - @linkml:Float ? ; - @linkml:Float ? ; - @linkml:Integer ? ; - @linkml:Integer ? ; - @linkml:Integer ? ; - @linkml:Integer ? ; - @linkml:Boolean ? ; - @linkml:Boolean ? - ) ; - rdf:type [ ] ? - ) -} - - CLOSED { - ( $ @ * ; - rdf:type [ ] ? - ) -} - - diff --git a/projects/class_enrichment/sqlschema/class_enrichment.sql b/projects/class_enrichment/sqlschema/class_enrichment.sql deleted file mode 100644 index dfc0b38dc..000000000 --- a/projects/class_enrichment/sqlschema/class_enrichment.sql +++ /dev/null @@ -1,29 +0,0 @@ - - -CREATE TABLE "ClassEnrichmentConfiguration" ( - p_value_cutoff FLOAT NOT NULL, - PRIMARY KEY (p_value_cutoff) -); - -CREATE TABLE "ClassEnrichmentResult" ( - class_id TEXT NOT NULL, - class_label TEXT, - rank INTEGER, - p_value FLOAT NOT NULL, - p_value_adjusted FLOAT, - false_discovery_rate FLOAT, - fold_enrichment FLOAT, - probability FLOAT, - sample_count INTEGER, - sample_total INTEGER, - background_count INTEGER, - background_total INTEGER, - ancestor_of_more_informative_result BOOLEAN, - descendant_of_more_informative_result BOOLEAN, - PRIMARY KEY (class_id, class_label, rank, p_value, p_value_adjusted, false_discovery_rate, fold_enrichment, probability, sample_count, sample_total, background_count, background_total, ancestor_of_more_informative_result, descendant_of_more_informative_result) -); - -CREATE TABLE "ClassEnrichmentResultSet" ( - results TEXT, - PRIMARY KEY (results) -); diff --git a/projects/composite_disease/composite_disease.py b/projects/composite_disease/composite_disease.py deleted file mode 100644 index 1b8a4a5c2..000000000 --- a/projects/composite_disease/composite_disease.py +++ /dev/null @@ -1,722 +0,0 @@ -# Auto generated from composite_disease.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:51:59 -# Schema: composite_disease -# -# id: http://w3id.org/ontogpt/composite_disease -# description: A template for representing composite disease concepts -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -HGNC = CurieNamespace('HGNC', 'http://example.org/UNKNOWN/HGNC/') -HP = CurieNamespace('HP', 'http://example.org/UNKNOWN/HP/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -COMPOSITE_DISEASE = CurieNamespace('composite_disease', 'http://w3id.org/ontogpt/composite_disease/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = COMPOSITE_DISEASE - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class GeneId(NamedEntityId): - pass - - -class SymptomId(NamedEntityId): - pass - - -class DiseaseId(NamedEntityId): - pass - - -class AdverseEffectId(NamedEntityId): - pass - - -class TreatmentId(NamedEntityId): - pass - - -class MechanismId(NamedEntityId): - pass - - -class DrugId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class CompositeDisease(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.CompositeDisease - class_class_curie: ClassVar[str] = "composite_disease:CompositeDisease" - class_name: ClassVar[str] = "CompositeDisease" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.CompositeDisease - - main_disease: Optional[Union[str, DiseaseId]] = None - drugs: Optional[Union[Union[str, DrugId], List[Union[str, DrugId]]]] = empty_list() - treatments: Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]] = empty_list() - contraindications: Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]] = empty_list() - treatment_mechanisms: Optional[Union[Union[dict, "TreatmentMechanism"], List[Union[dict, "TreatmentMechanism"]]]] = empty_list() - treatment_efficacies: Optional[Union[Union[dict, "TreatmentEfficacy"], List[Union[dict, "TreatmentEfficacy"]]]] = empty_list() - treatment_adverse_effects: Optional[Union[Union[dict, "TreatmentAdverseEffect"], List[Union[dict, "TreatmentAdverseEffect"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.main_disease is not None and not isinstance(self.main_disease, DiseaseId): - self.main_disease = DiseaseId(self.main_disease) - - if not isinstance(self.drugs, list): - self.drugs = [self.drugs] if self.drugs is not None else [] - self.drugs = [v if isinstance(v, DrugId) else DrugId(v) for v in self.drugs] - - if not isinstance(self.treatments, list): - self.treatments = [self.treatments] if self.treatments is not None else [] - self.treatments = [v if isinstance(v, TreatmentId) else TreatmentId(v) for v in self.treatments] - - if not isinstance(self.contraindications, list): - self.contraindications = [self.contraindications] if self.contraindications is not None else [] - self.contraindications = [v if isinstance(v, TreatmentId) else TreatmentId(v) for v in self.contraindications] - - if not isinstance(self.treatment_mechanisms, list): - self.treatment_mechanisms = [self.treatment_mechanisms] if self.treatment_mechanisms is not None else [] - self.treatment_mechanisms = [v if isinstance(v, TreatmentMechanism) else TreatmentMechanism(**as_dict(v)) for v in self.treatment_mechanisms] - - if not isinstance(self.treatment_efficacies, list): - self.treatment_efficacies = [self.treatment_efficacies] if self.treatment_efficacies is not None else [] - self.treatment_efficacies = [v if isinstance(v, TreatmentEfficacy) else TreatmentEfficacy(**as_dict(v)) for v in self.treatment_efficacies] - - if not isinstance(self.treatment_adverse_effects, list): - self.treatment_adverse_effects = [self.treatment_adverse_effects] if self.treatment_adverse_effects is not None else [] - self.treatment_adverse_effects = [v if isinstance(v, TreatmentAdverseEffect) else TreatmentAdverseEffect(**as_dict(v)) for v in self.treatment_adverse_effects] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Gene - class_class_curie: ClassVar[str] = "composite_disease:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Symptom(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Symptom - class_class_curie: ClassVar[str] = "composite_disease:Symptom" - class_name: ClassVar[str] = "Symptom" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Symptom - - id: Union[str, SymptomId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, SymptomId): - self.id = SymptomId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Disease(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Disease - class_class_curie: ClassVar[str] = "composite_disease:Disease" - class_name: ClassVar[str] = "Disease" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Disease - - id: Union[str, DiseaseId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiseaseId): - self.id = DiseaseId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class AdverseEffect(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.AdverseEffect - class_class_curie: ClassVar[str] = "composite_disease:AdverseEffect" - class_name: ClassVar[str] = "AdverseEffect" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.AdverseEffect - - id: Union[str, AdverseEffectId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, AdverseEffectId): - self.id = AdverseEffectId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Treatment(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Treatment - class_class_curie: ClassVar[str] = "composite_disease:Treatment" - class_name: ClassVar[str] = "Treatment" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Treatment - - id: Union[str, TreatmentId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, TreatmentId): - self.id = TreatmentId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Mechanism(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Mechanism - class_class_curie: ClassVar[str] = "composite_disease:Mechanism" - class_name: ClassVar[str] = "Mechanism" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Mechanism - - id: Union[str, MechanismId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MechanismId): - self.id = MechanismId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Drug(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Drug - class_class_curie: ClassVar[str] = "composite_disease:Drug" - class_name: ClassVar[str] = "Drug" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Drug - - id: Union[str, DrugId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DrugId): - self.id = DrugId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.CompoundExpression - - -@dataclass -class TreatmentMechanism(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.TreatmentMechanism - class_class_curie: ClassVar[str] = "composite_disease:TreatmentMechanism" - class_name: ClassVar[str] = "TreatmentMechanism" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.TreatmentMechanism - - treatment: Optional[Union[str, TreatmentId]] = None - mechanism: Optional[Union[str, MechanismId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.treatment is not None and not isinstance(self.treatment, TreatmentId): - self.treatment = TreatmentId(self.treatment) - - if self.mechanism is not None and not isinstance(self.mechanism, MechanismId): - self.mechanism = MechanismId(self.mechanism) - - super().__post_init__(**kwargs) - - -@dataclass -class TreatmentAdverseEffect(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.TreatmentAdverseEffect - class_class_curie: ClassVar[str] = "composite_disease:TreatmentAdverseEffect" - class_name: ClassVar[str] = "TreatmentAdverseEffect" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.TreatmentAdverseEffect - - treatment: Optional[Union[str, TreatmentId]] = None - adverse_effects: Optional[Union[Union[str, AdverseEffectId], List[Union[str, AdverseEffectId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.treatment is not None and not isinstance(self.treatment, TreatmentId): - self.treatment = TreatmentId(self.treatment) - - if not isinstance(self.adverse_effects, list): - self.adverse_effects = [self.adverse_effects] if self.adverse_effects is not None else [] - self.adverse_effects = [v if isinstance(v, AdverseEffectId) else AdverseEffectId(v) for v in self.adverse_effects] - - super().__post_init__(**kwargs) - - -@dataclass -class TreatmentEfficacy(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.TreatmentEfficacy - class_class_curie: ClassVar[str] = "composite_disease:TreatmentEfficacy" - class_name: ClassVar[str] = "TreatmentEfficacy" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.TreatmentEfficacy - - treatment: Optional[Union[str, TreatmentId]] = None - efficacy: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.treatment is not None and not isinstance(self.treatment, TreatmentId): - self.treatment = TreatmentId(self.treatment) - - if self.efficacy is not None and not isinstance(self.efficacy, str): - self.efficacy = str(self.efficacy) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = COMPOSITE_DISEASE.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NCITDrugType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="NCITDrugType", - ) - -class NCITTreatmentType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="NCITTreatmentType", - ) - -class NCITTActivityType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="NCITTActivityType", - ) - -class MAXOActionType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="MAXOActionType", - ) - -class MESHTherapeuticType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="MESHTherapeuticType", - ) - -class CHEBIDrugType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="CHEBIDrugType", - ) - -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.compositeDisease__main_disease = Slot(uri=COMPOSITE_DISEASE.main_disease, name="compositeDisease__main_disease", curie=COMPOSITE_DISEASE.curie('main_disease'), - model_uri=COMPOSITE_DISEASE.compositeDisease__main_disease, domain=None, range=Optional[Union[str, DiseaseId]]) - -slots.compositeDisease__drugs = Slot(uri=COMPOSITE_DISEASE.drugs, name="compositeDisease__drugs", curie=COMPOSITE_DISEASE.curie('drugs'), - model_uri=COMPOSITE_DISEASE.compositeDisease__drugs, domain=None, range=Optional[Union[Union[str, DrugId], List[Union[str, DrugId]]]]) - -slots.compositeDisease__treatments = Slot(uri=COMPOSITE_DISEASE.treatments, name="compositeDisease__treatments", curie=COMPOSITE_DISEASE.curie('treatments'), - model_uri=COMPOSITE_DISEASE.compositeDisease__treatments, domain=None, range=Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]]) - -slots.compositeDisease__contraindications = Slot(uri=COMPOSITE_DISEASE.contraindications, name="compositeDisease__contraindications", curie=COMPOSITE_DISEASE.curie('contraindications'), - model_uri=COMPOSITE_DISEASE.compositeDisease__contraindications, domain=None, range=Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]]) - -slots.compositeDisease__treatment_mechanisms = Slot(uri=COMPOSITE_DISEASE.treatment_mechanisms, name="compositeDisease__treatment_mechanisms", curie=COMPOSITE_DISEASE.curie('treatment_mechanisms'), - model_uri=COMPOSITE_DISEASE.compositeDisease__treatment_mechanisms, domain=None, range=Optional[Union[Union[dict, TreatmentMechanism], List[Union[dict, TreatmentMechanism]]]]) - -slots.compositeDisease__treatment_efficacies = Slot(uri=COMPOSITE_DISEASE.treatment_efficacies, name="compositeDisease__treatment_efficacies", curie=COMPOSITE_DISEASE.curie('treatment_efficacies'), - model_uri=COMPOSITE_DISEASE.compositeDisease__treatment_efficacies, domain=None, range=Optional[Union[Union[dict, TreatmentEfficacy], List[Union[dict, TreatmentEfficacy]]]]) - -slots.compositeDisease__treatment_adverse_effects = Slot(uri=COMPOSITE_DISEASE.treatment_adverse_effects, name="compositeDisease__treatment_adverse_effects", curie=COMPOSITE_DISEASE.curie('treatment_adverse_effects'), - model_uri=COMPOSITE_DISEASE.compositeDisease__treatment_adverse_effects, domain=None, range=Optional[Union[Union[dict, TreatmentAdverseEffect], List[Union[dict, TreatmentAdverseEffect]]]]) - -slots.treatmentMechanism__treatment = Slot(uri=COMPOSITE_DISEASE.treatment, name="treatmentMechanism__treatment", curie=COMPOSITE_DISEASE.curie('treatment'), - model_uri=COMPOSITE_DISEASE.treatmentMechanism__treatment, domain=None, range=Optional[Union[str, TreatmentId]]) - -slots.treatmentMechanism__mechanism = Slot(uri=COMPOSITE_DISEASE.mechanism, name="treatmentMechanism__mechanism", curie=COMPOSITE_DISEASE.curie('mechanism'), - model_uri=COMPOSITE_DISEASE.treatmentMechanism__mechanism, domain=None, range=Optional[Union[str, MechanismId]]) - -slots.treatmentAdverseEffect__treatment = Slot(uri=COMPOSITE_DISEASE.treatment, name="treatmentAdverseEffect__treatment", curie=COMPOSITE_DISEASE.curie('treatment'), - model_uri=COMPOSITE_DISEASE.treatmentAdverseEffect__treatment, domain=None, range=Optional[Union[str, TreatmentId]]) - -slots.treatmentAdverseEffect__adverse_effects = Slot(uri=COMPOSITE_DISEASE.adverse_effects, name="treatmentAdverseEffect__adverse_effects", curie=COMPOSITE_DISEASE.curie('adverse_effects'), - model_uri=COMPOSITE_DISEASE.treatmentAdverseEffect__adverse_effects, domain=None, range=Optional[Union[Union[str, AdverseEffectId], List[Union[str, AdverseEffectId]]]]) - -slots.treatmentEfficacy__treatment = Slot(uri=COMPOSITE_DISEASE.treatment, name="treatmentEfficacy__treatment", curie=COMPOSITE_DISEASE.curie('treatment'), - model_uri=COMPOSITE_DISEASE.treatmentEfficacy__treatment, domain=None, range=Optional[Union[str, TreatmentId]]) - -slots.treatmentEfficacy__efficacy = Slot(uri=COMPOSITE_DISEASE.efficacy, name="treatmentEfficacy__efficacy", curie=COMPOSITE_DISEASE.curie('efficacy'), - model_uri=COMPOSITE_DISEASE.treatmentEfficacy__efficacy, domain=None, range=Optional[str]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=COMPOSITE_DISEASE.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=COMPOSITE_DISEASE.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=COMPOSITE_DISEASE.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=COMPOSITE_DISEASE.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=COMPOSITE_DISEASE.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=COMPOSITE_DISEASE.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=COMPOSITE_DISEASE.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=COMPOSITE_DISEASE.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=COMPOSITE_DISEASE.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=COMPOSITE_DISEASE.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=COMPOSITE_DISEASE.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=COMPOSITE_DISEASE.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=COMPOSITE_DISEASE.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=COMPOSITE_DISEASE.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=COMPOSITE_DISEASE.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=COMPOSITE_DISEASE.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=COMPOSITE_DISEASE.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=COMPOSITE_DISEASE.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=COMPOSITE_DISEASE.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=COMPOSITE_DISEASE.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=COMPOSITE_DISEASE.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=COMPOSITE_DISEASE.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=COMPOSITE_DISEASE.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=COMPOSITE_DISEASE.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=COMPOSITE_DISEASE.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/composite_disease/docs/AdverseEffect.md b/projects/composite_disease/docs/AdverseEffect.md deleted file mode 100644 index d439f5a44..000000000 --- a/projects/composite_disease/docs/AdverseEffect.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: AdverseEffect - - - - -URI: [composite_disease:AdverseEffect](http://w3id.org/ontogpt/composite_disease/AdverseEffect) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[TreatmentAdverseEffect]-%20adverse_effects%200..*>[AdverseEffect|id(i):string;label(i):string%20%3F],[NamedEntity]^-[AdverseEffect],[TreatmentAdverseEffect])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[TreatmentAdverseEffect]-%20adverse_effects%200..*>[AdverseEffect|id(i):string;label(i):string%20%3F],[NamedEntity]^-[AdverseEffect],[TreatmentAdverseEffect]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞adverse_effects](treatmentAdverseEffect__adverse_effects.md)* 0..\* **[AdverseEffect](AdverseEffect.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/AnnotatorResult.md b/projects/composite_disease/docs/AnnotatorResult.md deleted file mode 100644 index b89c1a94d..000000000 --- a/projects/composite_disease/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [composite_disease:AnnotatorResult](http://w3id.org/ontogpt/composite_disease/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) 0..1 - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) 0..1 - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) 0..1 - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/Any.md b/projects/composite_disease/docs/Any.md deleted file mode 100644 index f5b564def..000000000 --- a/projects/composite_disease/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [composite_disease:Any](http://w3id.org/ontogpt/composite_disease/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* 0..1 **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* 0..\* **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/composite_disease/docs/CHEBIDrugType.md b/projects/composite_disease/docs/CHEBIDrugType.md deleted file mode 100644 index 4da395edc..000000000 --- a/projects/composite_disease/docs/CHEBIDrugType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: CHEBIDrugType - - - - -URI: [composite_disease:CHEBIDrugType](http://w3id.org/ontogpt/composite_disease/CHEBIDrugType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/composite_disease/docs/CompositeDisease.md b/projects/composite_disease/docs/CompositeDisease.md deleted file mode 100644 index edcff906b..000000000 --- a/projects/composite_disease/docs/CompositeDisease.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Class: CompositeDisease - - - - -URI: [composite_disease:CompositeDisease](http://w3id.org/ontogpt/composite_disease/CompositeDisease) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[Treatment],[Drug],[Disease],[TreatmentAdverseEffect]0..1 - * Description: the name of the disease that is treated. - * Range: [Disease](Disease.md) - * [➞drugs](compositeDisease__drugs.md) 0..\* - * Description: semicolon-separated list of named small molecule drugs - * Range: [Drug](Drug.md) - * [➞treatments](compositeDisease__treatments.md) 0..\* - * Description: semicolon-separated list of therapies and treatments are indicated for treating the disease. - * Range: [Treatment](Treatment.md) - * [➞contraindications](compositeDisease__contraindications.md) 0..\* - * Description: semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects. - * Range: [Treatment](Treatment.md) - * [➞treatment_mechanisms](compositeDisease__treatment_mechanisms.md) 0..\* - * Description: semicolon-separated list of treatment to asterisk-separated mechanism associations - * Range: [TreatmentMechanism](TreatmentMechanism.md) - * [➞treatment_efficacies](compositeDisease__treatment_efficacies.md) 0..\* - * Description: semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective - * Range: [TreatmentEfficacy](TreatmentEfficacy.md) - * [➞treatment_adverse_effects](compositeDisease__treatment_adverse_effects.md) 0..\* - * Description: semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea - * Range: [TreatmentAdverseEffect](TreatmentAdverseEffect.md) diff --git a/projects/composite_disease/docs/CompoundExpression.md b/projects/composite_disease/docs/CompoundExpression.md deleted file mode 100644 index d1831129e..000000000 --- a/projects/composite_disease/docs/CompoundExpression.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [composite_disease:CompoundExpression](http://w3id.org/ontogpt/composite_disease/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[CompoundExpression]^-[Triple],[CompoundExpression]^-[TreatmentMechanism],[CompoundExpression]^-[TreatmentEfficacy],[CompoundExpression]^-[TreatmentAdverseEffect])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[CompoundExpression]^-[Triple],[CompoundExpression]^-[TreatmentMechanism],[CompoundExpression]^-[TreatmentEfficacy],[CompoundExpression]^-[TreatmentAdverseEffect]) - -## Children - - * [TreatmentAdverseEffect](TreatmentAdverseEffect.md) - * [TreatmentEfficacy](TreatmentEfficacy.md) - * [TreatmentMechanism](TreatmentMechanism.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/composite_disease/docs/Disease.md b/projects/composite_disease/docs/Disease.md deleted file mode 100644 index 43817a43c..000000000 --- a/projects/composite_disease/docs/Disease.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Disease - - - - -URI: [composite_disease:Disease](http://w3id.org/ontogpt/composite_disease/Disease) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[CompositeDisease]-%20main_disease%200..1>[Disease|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Disease],[CompositeDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[CompositeDisease]-%20main_disease%200..1>[Disease|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Disease],[CompositeDisease]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞main_disease](compositeDisease__main_disease.md)* 0..1 **[Disease](Disease.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/Drug.md b/projects/composite_disease/docs/Drug.md deleted file mode 100644 index ff08bec35..000000000 --- a/projects/composite_disease/docs/Drug.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Drug - - - - -URI: [composite_disease:Drug](http://w3id.org/ontogpt/composite_disease/Drug) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[CompositeDisease]-%20drugs%200..*>[Drug|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Drug],[CompositeDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[CompositeDisease]-%20drugs%200..*>[Drug|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Drug],[CompositeDisease]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞drugs](compositeDisease__drugs.md)* 0..\* **[Drug](Drug.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/ExtractionResult.md b/projects/composite_disease/docs/ExtractionResult.md deleted file mode 100644 index e138c25b7..000000000 --- a/projects/composite_disease/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [composite_disease:ExtractionResult](http://w3id.org/ontogpt/composite_disease/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]0..1 - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) 0..1 - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) 0..1 - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) 0..1 - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) 0..1 - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) 0..1 - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) 0..\* - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/composite_disease/docs/Gene.md b/projects/composite_disease/docs/Gene.md deleted file mode 100644 index abeb93212..000000000 --- a/projects/composite_disease/docs/Gene.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Gene - - - - -URI: [composite_disease:Gene](http://w3id.org/ontogpt/composite_disease/Gene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[NamedEntity]^-[Gene|id(i):string;label(i):string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[NamedEntity]^-[Gene|id(i):string;label(i):string%20%3F]) - -## Identifier prefixes - - * HGNC - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/MAXOActionType.md b/projects/composite_disease/docs/MAXOActionType.md deleted file mode 100644 index cf61778da..000000000 --- a/projects/composite_disease/docs/MAXOActionType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: MAXOActionType - - - - -URI: [composite_disease:MAXOActionType](http://w3id.org/ontogpt/composite_disease/MAXOActionType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/composite_disease/docs/MESHTherapeuticType.md b/projects/composite_disease/docs/MESHTherapeuticType.md deleted file mode 100644 index d3e9d3dff..000000000 --- a/projects/composite_disease/docs/MESHTherapeuticType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: MESHTherapeuticType - - - - -URI: [composite_disease:MESHTherapeuticType](http://w3id.org/ontogpt/composite_disease/MESHTherapeuticType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/composite_disease/docs/Mechanism.md b/projects/composite_disease/docs/Mechanism.md deleted file mode 100644 index f19f1dbcb..000000000 --- a/projects/composite_disease/docs/Mechanism.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Mechanism - - - - -URI: [composite_disease:Mechanism](http://w3id.org/ontogpt/composite_disease/Mechanism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[TreatmentMechanism]-%20mechanism%200..1>[Mechanism|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Mechanism],[TreatmentMechanism])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[TreatmentMechanism]-%20mechanism%200..1>[Mechanism|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Mechanism],[TreatmentMechanism]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞mechanism](treatmentMechanism__mechanism.md)* 0..1 **[Mechanism](Mechanism.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/NCITDrugType.md b/projects/composite_disease/docs/NCITDrugType.md deleted file mode 100644 index 4a0d81963..000000000 --- a/projects/composite_disease/docs/NCITDrugType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: NCITDrugType - - - - -URI: [composite_disease:NCITDrugType](http://w3id.org/ontogpt/composite_disease/NCITDrugType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/composite_disease/docs/NCITTActivityType.md b/projects/composite_disease/docs/NCITTActivityType.md deleted file mode 100644 index da33466d9..000000000 --- a/projects/composite_disease/docs/NCITTActivityType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: NCITTActivityType - - - - -URI: [composite_disease:NCITTActivityType](http://w3id.org/ontogpt/composite_disease/NCITTActivityType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/composite_disease/docs/NCITTreatmentType.md b/projects/composite_disease/docs/NCITTreatmentType.md deleted file mode 100644 index 309c96759..000000000 --- a/projects/composite_disease/docs/NCITTreatmentType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: NCITTreatmentType - - - - -URI: [composite_disease:NCITTreatmentType](http://w3id.org/ontogpt/composite_disease/NCITTreatmentType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/composite_disease/docs/NamedEntity.md b/projects/composite_disease/docs/NamedEntity.md deleted file mode 100644 index 2ca5facd0..000000000 --- a/projects/composite_disease/docs/NamedEntity.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [composite_disease:NamedEntity](http://w3id.org/ontogpt/composite_disease/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Treatment],[Symptom],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Treatment],[NamedEntity]^-[Symptom],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Mechanism],[NamedEntity]^-[Gene],[NamedEntity]^-[Drug],[NamedEntity]^-[Disease],[NamedEntity]^-[AdverseEffect],[Triple],[Mechanism],[Gene],[Drug],[Disease],[AdverseEffect])](https://yuml.me/diagram/nofunky;dir:TB/class/[Treatment],[Symptom],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Treatment],[NamedEntity]^-[Symptom],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Mechanism],[NamedEntity]^-[Gene],[NamedEntity]^-[Drug],[NamedEntity]^-[Disease],[NamedEntity]^-[AdverseEffect],[Triple],[Mechanism],[Gene],[Drug],[Disease],[AdverseEffect]) - -## Children - - * [AdverseEffect](AdverseEffect.md) - * [Disease](Disease.md) - * [Drug](Drug.md) - * [Gene](Gene.md) - * [Mechanism](Mechanism.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - * [Treatment](Treatment.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* 0..1 **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/NullDataOptions.md b/projects/composite_disease/docs/NullDataOptions.md deleted file mode 100644 index e5a12b342..000000000 --- a/projects/composite_disease/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [composite_disease:NullDataOptions](http://w3id.org/ontogpt/composite_disease/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/composite_disease/docs/Publication.md b/projects/composite_disease/docs/Publication.md deleted file mode 100644 index 661829a48..000000000 --- a/projects/composite_disease/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [composite_disease:Publication](http://w3id.org/ontogpt/composite_disease/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* 0..1 **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) 0..1 - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) 0..1 - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) 0..1 - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) 0..1 - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) 0..1 - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/RelationshipType.md b/projects/composite_disease/docs/RelationshipType.md deleted file mode 100644 index 6b4c516bc..000000000 --- a/projects/composite_disease/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [composite_disease:RelationshipType](http://w3id.org/ontogpt/composite_disease/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* 0..1 **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/Symptom.md b/projects/composite_disease/docs/Symptom.md deleted file mode 100644 index 06440e5f1..000000000 --- a/projects/composite_disease/docs/Symptom.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Symptom - - - - -URI: [composite_disease:Symptom](http://w3id.org/ontogpt/composite_disease/Symptom) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]^-[Symptom|id(i):string;label(i):string%20%3F],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]^-[Symptom|id(i):string;label(i):string%20%3F],[NamedEntity]) - -## Identifier prefixes - - * HP - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/TextWithTriples.md b/projects/composite_disease/docs/TextWithTriples.md deleted file mode 100644 index 132154937..000000000 --- a/projects/composite_disease/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [composite_disease:TextWithTriples](http://w3id.org/ontogpt/composite_disease/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]0..1 - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) 0..\* - * Range: [Triple](Triple.md) diff --git a/projects/composite_disease/docs/Treatment.md b/projects/composite_disease/docs/Treatment.md deleted file mode 100644 index 74b7739fd..000000000 --- a/projects/composite_disease/docs/Treatment.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Treatment - - - - -URI: [composite_disease:Treatment](http://w3id.org/ontogpt/composite_disease/Treatment) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[CompositeDisease]-%20contraindications%200..*>[Treatment|id(i):string;label(i):string%20%3F],[CompositeDisease]-%20treatments%200..*>[Treatment],[TreatmentAdverseEffect]-%20treatment%200..1>[Treatment],[TreatmentEfficacy]-%20treatment%200..1>[Treatment],[TreatmentMechanism]-%20treatment%200..1>[Treatment],[NamedEntity]^-[Treatment],[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[NamedEntity],[CompositeDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[CompositeDisease]-%20contraindications%200..*>[Treatment|id(i):string;label(i):string%20%3F],[CompositeDisease]-%20treatments%200..*>[Treatment],[TreatmentAdverseEffect]-%20treatment%200..1>[Treatment],[TreatmentEfficacy]-%20treatment%200..1>[Treatment],[TreatmentMechanism]-%20treatment%200..1>[Treatment],[NamedEntity]^-[Treatment],[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[NamedEntity],[CompositeDisease]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞contraindications](compositeDisease__contraindications.md)* 0..\* **[Treatment](Treatment.md)** - * **None** *[➞treatments](compositeDisease__treatments.md)* 0..\* **[Treatment](Treatment.md)** - * **None** *[➞treatment](treatmentAdverseEffect__treatment.md)* 0..1 **[Treatment](Treatment.md)** - * **None** *[➞treatment](treatmentEfficacy__treatment.md)* 0..1 **[Treatment](Treatment.md)** - * **None** *[➞treatment](treatmentMechanism__treatment.md)* 0..1 **[Treatment](Treatment.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/TreatmentAdverseEffect.md b/projects/composite_disease/docs/TreatmentAdverseEffect.md deleted file mode 100644 index 5b6b0cdae..000000000 --- a/projects/composite_disease/docs/TreatmentAdverseEffect.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: TreatmentAdverseEffect - - - - -URI: [composite_disease:TreatmentAdverseEffect](http://w3id.org/ontogpt/composite_disease/TreatmentAdverseEffect) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AdverseEffect][TreatmentAdverseEffect],[CompoundExpression]^-[TreatmentAdverseEffect],[Treatment],[CompoundExpression],[CompositeDisease],[AdverseEffect])](https://yuml.me/diagram/nofunky;dir:TB/class/[AdverseEffect][TreatmentAdverseEffect],[CompoundExpression]^-[TreatmentAdverseEffect],[Treatment],[CompoundExpression],[CompositeDisease],[AdverseEffect]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞treatment_adverse_effects](compositeDisease__treatment_adverse_effects.md)* 0..\* **[TreatmentAdverseEffect](TreatmentAdverseEffect.md)** - -## Attributes - - -### Own - - * [➞treatment](treatmentAdverseEffect__treatment.md) 0..1 - * Range: [Treatment](Treatment.md) - * [➞adverse_effects](treatmentAdverseEffect__adverse_effects.md) 0..\* - * Range: [AdverseEffect](AdverseEffect.md) diff --git a/projects/composite_disease/docs/TreatmentEfficacy.md b/projects/composite_disease/docs/TreatmentEfficacy.md deleted file mode 100644 index b7bc0bf5a..000000000 --- a/projects/composite_disease/docs/TreatmentEfficacy.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: TreatmentEfficacy - - - - -URI: [composite_disease:TreatmentEfficacy](http://w3id.org/ontogpt/composite_disease/TreatmentEfficacy) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Treatment][TreatmentEfficacy],[CompoundExpression]^-[TreatmentEfficacy],[Treatment],[CompoundExpression],[CompositeDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[Treatment][TreatmentEfficacy],[CompoundExpression]^-[TreatmentEfficacy],[Treatment],[CompoundExpression],[CompositeDisease]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞treatment_efficacies](compositeDisease__treatment_efficacies.md)* 0..\* **[TreatmentEfficacy](TreatmentEfficacy.md)** - -## Attributes - - -### Own - - * [➞treatment](treatmentEfficacy__treatment.md) 0..1 - * Range: [Treatment](Treatment.md) - * [➞efficacy](treatmentEfficacy__efficacy.md) 0..1 - * Range: [String](types/String.md) diff --git a/projects/composite_disease/docs/TreatmentMechanism.md b/projects/composite_disease/docs/TreatmentMechanism.md deleted file mode 100644 index b8d82b890..000000000 --- a/projects/composite_disease/docs/TreatmentMechanism.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: TreatmentMechanism - - - - -URI: [composite_disease:TreatmentMechanism](http://w3id.org/ontogpt/composite_disease/TreatmentMechanism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Mechanism][TreatmentMechanism],[CompoundExpression]^-[TreatmentMechanism],[Treatment],[Mechanism],[CompoundExpression],[CompositeDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[Mechanism][TreatmentMechanism],[CompoundExpression]^-[TreatmentMechanism],[Treatment],[Mechanism],[CompoundExpression],[CompositeDisease]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞treatment_mechanisms](compositeDisease__treatment_mechanisms.md)* 0..\* **[TreatmentMechanism](TreatmentMechanism.md)** - -## Attributes - - -### Own - - * [➞treatment](treatmentMechanism__treatment.md) 0..1 - * Range: [Treatment](Treatment.md) - * [➞mechanism](treatmentMechanism__mechanism.md) 0..1 - * Range: [Mechanism](Mechanism.md) diff --git a/projects/composite_disease/docs/Triple.md b/projects/composite_disease/docs/Triple.md deleted file mode 100644 index e8018eeff..000000000 --- a/projects/composite_disease/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [composite_disease:Triple](http://w3id.org/ontogpt/composite_disease/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity][Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity][Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* 0..\* **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) 0..1 - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) 0..1 - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) 0..1 - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) 0..1 - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) 0..1 - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) 0..1 - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/composite_disease/docs/annotatorResult__object_id.md b/projects/composite_disease/docs/annotatorResult__object_id.md deleted file mode 100644 index 21c84bac5..000000000 --- a/projects/composite_disease/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [composite_disease:annotatorResult__object_id](http://w3id.org/ontogpt/composite_disease/annotatorResult__object_id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/composite_disease/docs/annotatorResult__object_text.md b/projects/composite_disease/docs/annotatorResult__object_text.md deleted file mode 100644 index 04eacc6a1..000000000 --- a/projects/composite_disease/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [composite_disease:annotatorResult__object_text](http://w3id.org/ontogpt/composite_disease/annotatorResult__object_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/composite_disease/docs/annotatorResult__subject_text.md b/projects/composite_disease/docs/annotatorResult__subject_text.md deleted file mode 100644 index 813a613dc..000000000 --- a/projects/composite_disease/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [composite_disease:annotatorResult__subject_text](http://w3id.org/ontogpt/composite_disease/annotatorResult__subject_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/composite_disease/docs/compositeDisease__contraindications.md b/projects/composite_disease/docs/compositeDisease__contraindications.md deleted file mode 100644 index b649b37bc..000000000 --- a/projects/composite_disease/docs/compositeDisease__contraindications.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: contraindications - - -semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects. - -URI: [composite_disease:compositeDisease__contraindications](http://w3id.org/ontogpt/composite_disease/compositeDisease__contraindications) - - -## Domain and Range - -None → 0..\* [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [CompositeDisease](CompositeDisease.md) diff --git a/projects/composite_disease/docs/compositeDisease__drugs.md b/projects/composite_disease/docs/compositeDisease__drugs.md deleted file mode 100644 index 0e62f267d..000000000 --- a/projects/composite_disease/docs/compositeDisease__drugs.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: drugs - - -semicolon-separated list of named small molecule drugs - -URI: [composite_disease:compositeDisease__drugs](http://w3id.org/ontogpt/composite_disease/compositeDisease__drugs) - - -## Domain and Range - -None → 0..\* [Drug](Drug.md) - -## Parents - - -## Children - - -## Used by - - * [CompositeDisease](CompositeDisease.md) diff --git a/projects/composite_disease/docs/compositeDisease__main_disease.md b/projects/composite_disease/docs/compositeDisease__main_disease.md deleted file mode 100644 index 46fb5d7f6..000000000 --- a/projects/composite_disease/docs/compositeDisease__main_disease.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: main_disease - - -the name of the disease that is treated. - -URI: [composite_disease:compositeDisease__main_disease](http://w3id.org/ontogpt/composite_disease/compositeDisease__main_disease) - - -## Domain and Range - -None → 0..1 [Disease](Disease.md) - -## Parents - - -## Children - - -## Used by - - * [CompositeDisease](CompositeDisease.md) diff --git a/projects/composite_disease/docs/compositeDisease__treatment_adverse_effects.md b/projects/composite_disease/docs/compositeDisease__treatment_adverse_effects.md deleted file mode 100644 index 59cc61e70..000000000 --- a/projects/composite_disease/docs/compositeDisease__treatment_adverse_effects.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment_adverse_effects - - -semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea - -URI: [composite_disease:compositeDisease__treatment_adverse_effects](http://w3id.org/ontogpt/composite_disease/compositeDisease__treatment_adverse_effects) - - -## Domain and Range - -None → 0..\* [TreatmentAdverseEffect](TreatmentAdverseEffect.md) - -## Parents - - -## Children - - -## Used by - - * [CompositeDisease](CompositeDisease.md) diff --git a/projects/composite_disease/docs/compositeDisease__treatment_efficacies.md b/projects/composite_disease/docs/compositeDisease__treatment_efficacies.md deleted file mode 100644 index 198fd7165..000000000 --- a/projects/composite_disease/docs/compositeDisease__treatment_efficacies.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment_efficacies - - -semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective - -URI: [composite_disease:compositeDisease__treatment_efficacies](http://w3id.org/ontogpt/composite_disease/compositeDisease__treatment_efficacies) - - -## Domain and Range - -None → 0..\* [TreatmentEfficacy](TreatmentEfficacy.md) - -## Parents - - -## Children - - -## Used by - - * [CompositeDisease](CompositeDisease.md) diff --git a/projects/composite_disease/docs/compositeDisease__treatment_mechanisms.md b/projects/composite_disease/docs/compositeDisease__treatment_mechanisms.md deleted file mode 100644 index 6634185bf..000000000 --- a/projects/composite_disease/docs/compositeDisease__treatment_mechanisms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment_mechanisms - - -semicolon-separated list of treatment to asterisk-separated mechanism associations - -URI: [composite_disease:compositeDisease__treatment_mechanisms](http://w3id.org/ontogpt/composite_disease/compositeDisease__treatment_mechanisms) - - -## Domain and Range - -None → 0..\* [TreatmentMechanism](TreatmentMechanism.md) - -## Parents - - -## Children - - -## Used by - - * [CompositeDisease](CompositeDisease.md) diff --git a/projects/composite_disease/docs/compositeDisease__treatments.md b/projects/composite_disease/docs/compositeDisease__treatments.md deleted file mode 100644 index 3b120d777..000000000 --- a/projects/composite_disease/docs/compositeDisease__treatments.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatments - - -semicolon-separated list of therapies and treatments are indicated for treating the disease. - -URI: [composite_disease:compositeDisease__treatments](http://w3id.org/ontogpt/composite_disease/compositeDisease__treatments) - - -## Domain and Range - -None → 0..\* [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [CompositeDisease](CompositeDisease.md) diff --git a/projects/composite_disease/docs/composite_disease.md b/projects/composite_disease/docs/composite_disease.md deleted file mode 100644 index a9c889f9f..000000000 --- a/projects/composite_disease/docs/composite_disease.md +++ /dev/null @@ -1,133 +0,0 @@ - -# composite_disease - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for representing composite disease concepts - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompositeDisease](CompositeDisease.md) - * [CompoundExpression](CompoundExpression.md) - * [TreatmentAdverseEffect](TreatmentAdverseEffect.md) - * [TreatmentEfficacy](TreatmentEfficacy.md) - * [TreatmentMechanism](TreatmentMechanism.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [AdverseEffect](AdverseEffect.md) - * [Disease](Disease.md) - * [Drug](Drug.md) - * [Gene](Gene.md) - * [Mechanism](Mechanism.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - * [Treatment](Treatment.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞contraindications](compositeDisease__contraindications.md) - semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects. - * [➞drugs](compositeDisease__drugs.md) - semicolon-separated list of named small molecule drugs - * [➞main_disease](compositeDisease__main_disease.md) - the name of the disease that is treated. - * [➞treatment_adverse_effects](compositeDisease__treatment_adverse_effects.md) - semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea - * [➞treatment_efficacies](compositeDisease__treatment_efficacies.md) - semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective - * [➞treatment_mechanisms](compositeDisease__treatment_mechanisms.md) - semicolon-separated list of treatment to asterisk-separated mechanism associations - * [➞treatments](compositeDisease__treatments.md) - semicolon-separated list of therapies and treatments are indicated for treating the disease. - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞adverse_effects](treatmentAdverseEffect__adverse_effects.md) - * [➞treatment](treatmentAdverseEffect__treatment.md) - * [➞efficacy](treatmentEfficacy__efficacy.md) - * [➞treatment](treatmentEfficacy__treatment.md) - * [➞mechanism](treatmentMechanism__mechanism.md) - * [➞treatment](treatmentMechanism__treatment.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [CHEBIDrugType](CHEBIDrugType.md) - * [MAXOActionType](MAXOActionType.md) - * [MESHTherapeuticType](MESHTherapeuticType.md) - * [NCITDrugType](NCITDrugType.md) - * [NCITTActivityType](NCITTActivityType.md) - * [NCITTreatmentType](NCITTreatmentType.md) - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/composite_disease/docs/extractionResult__extracted_object.md b/projects/composite_disease/docs/extractionResult__extracted_object.md deleted file mode 100644 index a085be898..000000000 --- a/projects/composite_disease/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [composite_disease:extractionResult__extracted_object](http://w3id.org/ontogpt/composite_disease/extractionResult__extracted_object) - - -## Domain and Range - -None → 0..1 [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/composite_disease/docs/extractionResult__input_id.md b/projects/composite_disease/docs/extractionResult__input_id.md deleted file mode 100644 index 236703e9a..000000000 --- a/projects/composite_disease/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [composite_disease:extractionResult__input_id](http://w3id.org/ontogpt/composite_disease/extractionResult__input_id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/composite_disease/docs/extractionResult__input_text.md b/projects/composite_disease/docs/extractionResult__input_text.md deleted file mode 100644 index e6400df0f..000000000 --- a/projects/composite_disease/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [composite_disease:extractionResult__input_text](http://w3id.org/ontogpt/composite_disease/extractionResult__input_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/composite_disease/docs/extractionResult__input_title.md b/projects/composite_disease/docs/extractionResult__input_title.md deleted file mode 100644 index 52f346e83..000000000 --- a/projects/composite_disease/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [composite_disease:extractionResult__input_title](http://w3id.org/ontogpt/composite_disease/extractionResult__input_title) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/composite_disease/docs/extractionResult__named_entities.md b/projects/composite_disease/docs/extractionResult__named_entities.md deleted file mode 100644 index e5a31210b..000000000 --- a/projects/composite_disease/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [composite_disease:extractionResult__named_entities](http://w3id.org/ontogpt/composite_disease/extractionResult__named_entities) - - -## Domain and Range - -None → 0..\* [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/composite_disease/docs/extractionResult__prompt.md b/projects/composite_disease/docs/extractionResult__prompt.md deleted file mode 100644 index 8b6ea40a1..000000000 --- a/projects/composite_disease/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [composite_disease:extractionResult__prompt](http://w3id.org/ontogpt/composite_disease/extractionResult__prompt) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/composite_disease/docs/extractionResult__raw_completion_output.md b/projects/composite_disease/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index c67f7ef5c..000000000 --- a/projects/composite_disease/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [composite_disease:extractionResult__raw_completion_output](http://w3id.org/ontogpt/composite_disease/extractionResult__raw_completion_output) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/composite_disease/docs/namedEntity__id.md b/projects/composite_disease/docs/namedEntity__id.md deleted file mode 100644 index 588564cf2..000000000 --- a/projects/composite_disease/docs/namedEntity__id.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [composite_disease:namedEntity__id](http://w3id.org/ontogpt/composite_disease/namedEntity__id) - - -## Domain and Range - -None → 1..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AdverseEffect](AdverseEffect.md) - * [Disease](Disease.md) - * [Drug](Drug.md) - * [Gene](Gene.md) - * [Mechanism](Mechanism.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - * [Treatment](Treatment.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/composite_disease/docs/namedEntity__label.md b/projects/composite_disease/docs/namedEntity__label.md deleted file mode 100644 index 9cfef98e0..000000000 --- a/projects/composite_disease/docs/namedEntity__label.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [composite_disease:namedEntity__label](http://w3id.org/ontogpt/composite_disease/namedEntity__label) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AdverseEffect](AdverseEffect.md) - * [Disease](Disease.md) - * [Drug](Drug.md) - * [Gene](Gene.md) - * [Mechanism](Mechanism.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - * [Treatment](Treatment.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/composite_disease/docs/publication__abstract.md b/projects/composite_disease/docs/publication__abstract.md deleted file mode 100644 index 74bb27221..000000000 --- a/projects/composite_disease/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [composite_disease:publication__abstract](http://w3id.org/ontogpt/composite_disease/publication__abstract) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/composite_disease/docs/publication__combined_text.md b/projects/composite_disease/docs/publication__combined_text.md deleted file mode 100644 index 7ba220d45..000000000 --- a/projects/composite_disease/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [composite_disease:publication__combined_text](http://w3id.org/ontogpt/composite_disease/publication__combined_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/composite_disease/docs/publication__full_text.md b/projects/composite_disease/docs/publication__full_text.md deleted file mode 100644 index 1053a20bb..000000000 --- a/projects/composite_disease/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [composite_disease:publication__full_text](http://w3id.org/ontogpt/composite_disease/publication__full_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/composite_disease/docs/publication__id.md b/projects/composite_disease/docs/publication__id.md deleted file mode 100644 index 06213aeab..000000000 --- a/projects/composite_disease/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [composite_disease:publication__id](http://w3id.org/ontogpt/composite_disease/publication__id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/composite_disease/docs/publication__title.md b/projects/composite_disease/docs/publication__title.md deleted file mode 100644 index a04d513a6..000000000 --- a/projects/composite_disease/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [composite_disease:publication__title](http://w3id.org/ontogpt/composite_disease/publication__title) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/composite_disease/docs/textWithTriples__publication.md b/projects/composite_disease/docs/textWithTriples__publication.md deleted file mode 100644 index 60bd567fb..000000000 --- a/projects/composite_disease/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [composite_disease:textWithTriples__publication](http://w3id.org/ontogpt/composite_disease/textWithTriples__publication) - - -## Domain and Range - -None → 0..1 [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/composite_disease/docs/textWithTriples__triples.md b/projects/composite_disease/docs/textWithTriples__triples.md deleted file mode 100644 index a05e900ee..000000000 --- a/projects/composite_disease/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [composite_disease:textWithTriples__triples](http://w3id.org/ontogpt/composite_disease/textWithTriples__triples) - - -## Domain and Range - -None → 0..\* [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/composite_disease/docs/treatmentAdverseEffect__adverse_effects.md b/projects/composite_disease/docs/treatmentAdverseEffect__adverse_effects.md deleted file mode 100644 index bca39a2dd..000000000 --- a/projects/composite_disease/docs/treatmentAdverseEffect__adverse_effects.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: adverse_effects - - - - -URI: [composite_disease:treatmentAdverseEffect__adverse_effects](http://w3id.org/ontogpt/composite_disease/treatmentAdverseEffect__adverse_effects) - - -## Domain and Range - -None → 0..\* [AdverseEffect](AdverseEffect.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentAdverseEffect](TreatmentAdverseEffect.md) diff --git a/projects/composite_disease/docs/treatmentAdverseEffect__treatment.md b/projects/composite_disease/docs/treatmentAdverseEffect__treatment.md deleted file mode 100644 index 8fa143a94..000000000 --- a/projects/composite_disease/docs/treatmentAdverseEffect__treatment.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment - - - - -URI: [composite_disease:treatmentAdverseEffect__treatment](http://w3id.org/ontogpt/composite_disease/treatmentAdverseEffect__treatment) - - -## Domain and Range - -None → 0..1 [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentAdverseEffect](TreatmentAdverseEffect.md) diff --git a/projects/composite_disease/docs/treatmentEfficacy__efficacy.md b/projects/composite_disease/docs/treatmentEfficacy__efficacy.md deleted file mode 100644 index 7d393ac11..000000000 --- a/projects/composite_disease/docs/treatmentEfficacy__efficacy.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: efficacy - - - - -URI: [composite_disease:treatmentEfficacy__efficacy](http://w3id.org/ontogpt/composite_disease/treatmentEfficacy__efficacy) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentEfficacy](TreatmentEfficacy.md) diff --git a/projects/composite_disease/docs/treatmentEfficacy__treatment.md b/projects/composite_disease/docs/treatmentEfficacy__treatment.md deleted file mode 100644 index 7abd2a6b6..000000000 --- a/projects/composite_disease/docs/treatmentEfficacy__treatment.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment - - - - -URI: [composite_disease:treatmentEfficacy__treatment](http://w3id.org/ontogpt/composite_disease/treatmentEfficacy__treatment) - - -## Domain and Range - -None → 0..1 [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentEfficacy](TreatmentEfficacy.md) diff --git a/projects/composite_disease/docs/treatmentMechanism__mechanism.md b/projects/composite_disease/docs/treatmentMechanism__mechanism.md deleted file mode 100644 index 39837c489..000000000 --- a/projects/composite_disease/docs/treatmentMechanism__mechanism.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: mechanism - - - - -URI: [composite_disease:treatmentMechanism__mechanism](http://w3id.org/ontogpt/composite_disease/treatmentMechanism__mechanism) - - -## Domain and Range - -None → 0..1 [Mechanism](Mechanism.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentMechanism](TreatmentMechanism.md) diff --git a/projects/composite_disease/docs/treatmentMechanism__treatment.md b/projects/composite_disease/docs/treatmentMechanism__treatment.md deleted file mode 100644 index eb85895d5..000000000 --- a/projects/composite_disease/docs/treatmentMechanism__treatment.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment - - - - -URI: [composite_disease:treatmentMechanism__treatment](http://w3id.org/ontogpt/composite_disease/treatmentMechanism__treatment) - - -## Domain and Range - -None → 0..1 [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentMechanism](TreatmentMechanism.md) diff --git a/projects/composite_disease/docs/triple__object.md b/projects/composite_disease/docs/triple__object.md deleted file mode 100644 index 3345909a5..000000000 --- a/projects/composite_disease/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [composite_disease:triple__object](http://w3id.org/ontogpt/composite_disease/triple__object) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/composite_disease/docs/triple__object_qualifier.md b/projects/composite_disease/docs/triple__object_qualifier.md deleted file mode 100644 index ff66108e0..000000000 --- a/projects/composite_disease/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [composite_disease:triple__object_qualifier](http://w3id.org/ontogpt/composite_disease/triple__object_qualifier) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/composite_disease/docs/triple__predicate.md b/projects/composite_disease/docs/triple__predicate.md deleted file mode 100644 index 427e1e3a2..000000000 --- a/projects/composite_disease/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [composite_disease:triple__predicate](http://w3id.org/ontogpt/composite_disease/triple__predicate) - - -## Domain and Range - -None → 0..1 [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/composite_disease/docs/triple__qualifier.md b/projects/composite_disease/docs/triple__qualifier.md deleted file mode 100644 index 9cc2b96e6..000000000 --- a/projects/composite_disease/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [composite_disease:triple__qualifier](http://w3id.org/ontogpt/composite_disease/triple__qualifier) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/composite_disease/docs/triple__subject.md b/projects/composite_disease/docs/triple__subject.md deleted file mode 100644 index ae60b051d..000000000 --- a/projects/composite_disease/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [composite_disease:triple__subject](http://w3id.org/ontogpt/composite_disease/triple__subject) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/composite_disease/docs/triple__subject_qualifier.md b/projects/composite_disease/docs/triple__subject_qualifier.md deleted file mode 100644 index 5051e8af0..000000000 --- a/projects/composite_disease/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [composite_disease:triple__subject_qualifier](http://w3id.org/ontogpt/composite_disease/triple__subject_qualifier) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/composite_disease/docs/types/Boolean.md b/projects/composite_disease/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/composite_disease/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/composite_disease/docs/types/Curie.md b/projects/composite_disease/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/composite_disease/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/composite_disease/docs/types/Date.md b/projects/composite_disease/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/composite_disease/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/composite_disease/docs/types/DateOrDatetime.md b/projects/composite_disease/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/composite_disease/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/composite_disease/docs/types/Datetime.md b/projects/composite_disease/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/composite_disease/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/composite_disease/docs/types/Decimal.md b/projects/composite_disease/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/composite_disease/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/composite_disease/docs/types/Double.md b/projects/composite_disease/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/composite_disease/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/composite_disease/docs/types/Float.md b/projects/composite_disease/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/composite_disease/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/composite_disease/docs/types/Integer.md b/projects/composite_disease/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/composite_disease/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/composite_disease/docs/types/Jsonpath.md b/projects/composite_disease/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/composite_disease/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/composite_disease/docs/types/Jsonpointer.md b/projects/composite_disease/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/composite_disease/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/composite_disease/docs/types/Ncname.md b/projects/composite_disease/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/composite_disease/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/composite_disease/docs/types/Nodeidentifier.md b/projects/composite_disease/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/composite_disease/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/composite_disease/docs/types/Objectidentifier.md b/projects/composite_disease/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/composite_disease/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/composite_disease/docs/types/Sparqlpath.md b/projects/composite_disease/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/composite_disease/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/composite_disease/docs/types/String.md b/projects/composite_disease/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/composite_disease/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/composite_disease/docs/types/Time.md b/projects/composite_disease/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/composite_disease/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/composite_disease/docs/types/Uri.md b/projects/composite_disease/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/composite_disease/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/composite_disease/docs/types/Uriorcurie.md b/projects/composite_disease/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/composite_disease/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/composite_disease/excel/composite_disease.xlsx b/projects/composite_disease/excel/composite_disease.xlsx deleted file mode 100644 index a1a5e49e8a579a67be549807a0524a55f340d91a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 12566 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z{t5F8^KqDa?fN0iL(TOkOaUO6AGs!mN5l7_;P?~f1fZNe2J>kAK9szE!qnnC4)ebT z@SSk;$KmP4f%iDfqY?a2h4=|mf&VznqapmTVg3mtL-;t%qcQxj+xrs+c!ua6=4bEs z(8&*r^`A?XNPa2ZA1-`Y{Qg|XOZw;5|0snYE`C_<{9GIim|X|N#BYk9hd2-O{ZE_` d3Lv0IvcHT3IAB2jPWgTUlneNzN_qF~e*kGCNUi_? diff --git a/projects/composite_disease/graphql/composite_disease.graphql b/projects/composite_disease/graphql/composite_disease.graphql deleted file mode 100644 index 7361ada27..000000000 --- a/projects/composite_disease/graphql/composite_disease.graphql +++ /dev/null @@ -1,134 +0,0 @@ -type AdverseEffect - { - id: String! - label: String - } - -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type CompositeDisease - { - mainDisease: Disease - drugs: [Drug] - treatments: [Treatment] - contraindications: [Treatment] - treatmentMechanisms: [TreatmentMechanism] - treatmentEfficacies: [TreatmentEfficacy] - treatmentAdverseEffects: [TreatmentAdverseEffect] - } - -interface CompoundExpression - { - } - -type Disease - { - id: String! - label: String - } - -type Drug - { - id: String! - label: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Gene - { - id: String! - label: String - } - -type Mechanism - { - id: String! - label: String - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type Symptom - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -type Treatment - { - id: String! - label: String - } - -type TreatmentAdverseEffect - { - treatment: Treatment - adverseEffects: [AdverseEffect] - } - -type TreatmentEfficacy - { - treatment: Treatment - efficacy: String - } - -type TreatmentMechanism - { - treatment: Treatment - mechanism: Mechanism - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/composite_disease/jsonld/composite_disease.context.jsonld b/projects/composite_disease/jsonld/composite_disease.context.jsonld deleted file mode 100644 index b1b6f5456..000000000 --- a/projects/composite_disease/jsonld/composite_disease.context.jsonld +++ /dev/null @@ -1,159 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:51:49", - "source": "composite_disease.yaml" - }, - "@context": { - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "HP": "http://example.org/UNKNOWN/HP/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "composite_disease": "http://w3id.org/ontogpt/composite_disease/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/composite_disease/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "contraindications": { - "@type": "@id" - }, - "drugs": { - "@type": "@id" - }, - "main_disease": { - "@type": "@id" - }, - "treatment_adverse_effects": { - "@type": "@id" - }, - "treatment_efficacies": { - "@type": "@id" - }, - "treatment_mechanisms": { - "@type": "@id" - }, - "treatments": { - "@type": "@id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "adverse_effects": { - "@type": "@id" - }, - "treatment": { - "@type": "@id" - }, - "mechanism": { - "@type": "@id" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/composite_disease/jsonld/composite_disease.jsonld b/projects/composite_disease/jsonld/composite_disease.jsonld deleted file mode 100644 index 05fbc5bff..000000000 --- a/projects/composite_disease/jsonld/composite_disease.jsonld +++ /dev/null @@ -1,1586 +0,0 @@ -{ - "name": "composite_disease", - "description": "A template for representing composite disease concepts", - "title": "Composite Disease", - "id": "http://w3id.org/ontogpt/composite_disease", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "composite_disease", - "prefix_reference": "http://w3id.org/ontogpt/composite_disease/" - } - ], - "default_prefix": "composite_disease", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NCITDrugType", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/NCITDrugType", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "reachable_from": { - "source_ontology": "obo:ncit", - "source_nodes": [ - "NCIT:C1908" - ] - } - }, - { - "name": "NCITTreatmentType", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/NCITTreatmentType", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "reachable_from": { - "source_ontology": "obo:ncit", - "source_nodes": [ - "NCIT:C25218" - ] - } - }, - { - "name": "NCITTActivityType", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/NCITTActivityType", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "reachable_from": { - "source_ontology": "obo:ncit", - "source_nodes": [ - "NCIT:C43431" - ] - } - }, - { - "name": "MAXOActionType", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/MAXOActionType", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "reachable_from": { - "source_ontology": "obo:maxo", - "source_nodes": [ - "MAXO:0000001" - ] - } - }, - { - "name": "MESHTherapeuticType", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/MESHTherapeuticType", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "reachable_from": { - "source_ontology": "obo:mesh", - "source_nodes": [ - "MESH:D013812" - ] - } - }, - { - "name": "CHEBIDrugType", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/CHEBIDrugType", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "reachable_from": { - "source_ontology": "obo:chebi", - "source_nodes": [ - "CHEBI:23888" - ], - "relationship_types": [ - "rdfs:subClassOf", - "RO:0000087" - ] - } - }, - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "compositeDisease__main_disease", - "description": "the name of the disease that is treated.", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/main_disease", - "alias": "main_disease", - "owner": "CompositeDisease", - "domain_of": [ - "CompositeDisease" - ], - "range": "Disease", - "@type": "SlotDefinition" - }, - { - "name": "compositeDisease__drugs", - "description": "semicolon-separated list of named small molecule drugs", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/drugs", - "multivalued": true, - "alias": "drugs", - "owner": "CompositeDisease", - "domain_of": [ - "CompositeDisease" - ], - "range": "Drug", - "@type": "SlotDefinition" - }, - { - "name": "compositeDisease__treatments", - "annotations": [ - { - "tag": "prompt.examples", - "value": "Imatinib, exercise, surgery", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of therapies and treatments are indicated for treating the disease.", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/treatments", - "multivalued": true, - "alias": "treatments", - "owner": "CompositeDisease", - "domain_of": [ - "CompositeDisease" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "compositeDisease__contraindications", - "annotations": [ - { - "tag": "prompt.examples", - "value": "Beta-blockers, exercise, surgery", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/contraindications", - "multivalued": true, - "alias": "contraindications", - "owner": "CompositeDisease", - "domain_of": [ - "CompositeDisease" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "compositeDisease__treatment_mechanisms", - "annotations": [ - { - "tag": "prompt.separator", - "value": "*", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of treatment to asterisk-separated mechanism associations", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/treatment_mechanisms", - "multivalued": true, - "alias": "treatment_mechanisms", - "owner": "CompositeDisease", - "domain_of": [ - "CompositeDisease" - ], - "range": "TreatmentMechanism", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "compositeDisease__treatment_efficacies", - "annotations": [ - { - "tag": "prompt.separator", - "value": "*", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/treatment_efficacies", - "multivalued": true, - "alias": "treatment_efficacies", - "owner": "CompositeDisease", - "domain_of": [ - "CompositeDisease" - ], - "range": "TreatmentEfficacy", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "compositeDisease__treatment_adverse_effects", - "annotations": [ - { - "tag": "prompt.separator", - "value": "*", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/treatment_adverse_effects", - "multivalued": true, - "alias": "treatment_adverse_effects", - "owner": "CompositeDisease", - "domain_of": [ - "CompositeDisease" - ], - "range": "TreatmentAdverseEffect", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "treatmentMechanism__treatment", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/treatment", - "alias": "treatment", - "owner": "TreatmentMechanism", - "domain_of": [ - "TreatmentMechanism" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "treatmentMechanism__mechanism", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/mechanism", - "alias": "mechanism", - "owner": "TreatmentMechanism", - "domain_of": [ - "TreatmentMechanism" - ], - "range": "Mechanism", - "@type": "SlotDefinition" - }, - { - "name": "treatmentAdverseEffect__treatment", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/treatment", - "alias": "treatment", - "owner": "TreatmentAdverseEffect", - "domain_of": [ - "TreatmentAdverseEffect" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "treatmentAdverseEffect__adverse_effects", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/adverse_effects", - "multivalued": true, - "alias": "adverse_effects", - "owner": "TreatmentAdverseEffect", - "domain_of": [ - "TreatmentAdverseEffect" - ], - "range": "AdverseEffect", - "@type": "SlotDefinition" - }, - { - "name": "treatmentEfficacy__treatment", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/treatment", - "alias": "treatment", - "owner": "TreatmentEfficacy", - "domain_of": [ - "TreatmentEfficacy" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "treatmentEfficacy__efficacy", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slot_uri": "http://w3id.org/ontogpt/composite_disease/efficacy", - "alias": "efficacy", - "owner": "TreatmentEfficacy", - "domain_of": [ - "TreatmentEfficacy" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": 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"annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "CompositeDisease", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/CompositeDisease", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "slots": [ - "compositeDisease__main_disease", - "compositeDisease__drugs", - "compositeDisease__treatments", - "compositeDisease__contraindications", - "compositeDisease__treatment_mechanisms", - 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"http://w3id.org/ontogpt/composite_disease/AdverseEffect", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:hp, sqlite:obo:ncit", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/composite_disease/AdverseEffect", - "@type": "ClassDefinition" - }, - { - "name": "Treatment", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/Treatment", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "is_a": "NamedEntity", - "values_from": [ - "NCITDrugType", - "NCITTreatmentType", - "NCITActivityType", - "MAXOTreatmentType", - "MESHTherapeuticType", - "CHEBIDrugType" - ], - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/composite_disease/Treatment", - "@type": "ClassDefinition" - }, - { - "name": "Mechanism", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/Mechanism", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/composite_disease/Mechanism", - "@type": "ClassDefinition" - }, - { - "name": "Drug", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/Drug", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:chebi, sqlite:obo:drugbank", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/composite_disease/Drug", - "@type": "ClassDefinition" - }, - { - "name": "TreatmentMechanism", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/TreatmentMechanism", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "is_a": "CompoundExpression", - "slots": [ - "treatmentMechanism__treatment", - "treatmentMechanism__mechanism" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "treatment", - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "mechanism", - "range": "Mechanism", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/composite_disease/TreatmentMechanism", - "@type": "ClassDefinition" - }, - { - "name": "TreatmentAdverseEffect", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/TreatmentAdverseEffect", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "is_a": "CompoundExpression", - "slots": [ - "treatmentAdverseEffect__treatment", - "treatmentAdverseEffect__adverse_effects" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "treatment", - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "adverse_effects", - "multivalued": true, - "range": "AdverseEffect", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/composite_disease/TreatmentAdverseEffect", - "@type": "ClassDefinition" - }, - { - "name": "TreatmentEfficacy", - "definition_uri": "http://w3id.org/ontogpt/composite_disease/TreatmentEfficacy", - "from_schema": "http://w3id.org/ontogpt/composite_disease", - "is_a": "CompoundExpression", - "slots": [ - "treatmentEfficacy__treatment", - "treatmentEfficacy__efficacy" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "treatment", - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "efficacy", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/composite_disease/TreatmentEfficacy", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - 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"prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "composite_disease.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 4519, - "generation_date": "2023-08-07T10:51:50", - "keywords": [ - "disease", - "indication" - ], - "@type": "SchemaDefinition", - "@context": [ - "projects/composite_disease/jsonld/composite_disease.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/composite_disease/" - } - ] -} diff --git a/projects/composite_disease/jsonschema/composite_disease.schema.json b/projects/composite_disease/jsonschema/composite_disease.schema.json deleted file mode 100644 index 10c5cd549..000000000 --- a/projects/composite_disease/jsonschema/composite_disease.schema.json +++ /dev/null @@ -1,457 +0,0 @@ -{ - "$defs": { - "AdverseEffect": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "AdverseEffect", - "type": "object" - }, - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "CHEBIDrugType": { - "description": "", - "enum": [], - "title": "CHEBIDrugType", - "type": "string" - }, - "CompositeDisease": { - "additionalProperties": false, - "description": "", - "properties": { - "contraindications": { - "description": "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.", - "items": { - "type": "string" - }, - "type": "array" - }, - "drugs": { - "description": "semicolon-separated list of named small molecule drugs", - "items": { - "type": "string" - }, - "type": "array" - }, - "main_disease": { - "description": "the name of the disease that is treated.", - "type": "string" - }, - "treatment_adverse_effects": { - "description": "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea", - "items": { - "$ref": "#/$defs/TreatmentAdverseEffect" - }, - "type": "array" - }, - "treatment_efficacies": { - "description": "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective", - "items": { - "$ref": "#/$defs/TreatmentEfficacy" - }, - "type": "array" - }, - "treatment_mechanisms": { - "description": "semicolon-separated list of treatment to asterisk-separated mechanism associations", - "items": { - "$ref": "#/$defs/TreatmentMechanism" - }, - "type": "array" - }, - "treatments": { - "description": "semicolon-separated list of therapies and treatments are indicated for treating the disease.", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "CompositeDisease", - "type": "object" - }, - "Disease": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Disease", - "type": "object" - }, - "Drug": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Drug", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Gene": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Gene", - "type": "object" - }, - "MAXOActionType": { - "description": "", - "enum": [], - "title": "MAXOActionType", - "type": "string" - }, - "MESHTherapeuticType": { - "description": "", - "enum": [], - "title": "MESHTherapeuticType", - "type": "string" - }, - "Mechanism": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Mechanism", - "type": "object" - }, - "NCITDrugType": { - "description": "", - "enum": [], - "title": "NCITDrugType", - "type": "string" - }, - "NCITTActivityType": { - "description": "", - "enum": [], - "title": "NCITTActivityType", - "type": "string" - }, - "NCITTreatmentType": { - "description": "", - "enum": [], - "title": "NCITTreatmentType", - "type": "string" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "Symptom": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Symptom", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Treatment": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Treatment", - "type": "object" - }, - "TreatmentAdverseEffect": { - "additionalProperties": false, - "description": "", - "properties": { - "adverse_effects": { - "items": { - "type": "string" - }, - "type": "array" - }, - "treatment": { - "type": "string" - } - }, - "title": "TreatmentAdverseEffect", - "type": "object" - }, - "TreatmentEfficacy": { - "additionalProperties": false, - "description": "", - "properties": { - "efficacy": { - "type": "string" - }, - "treatment": { - "type": "string" - } - }, - "title": "TreatmentEfficacy", - "type": "object" - }, - "TreatmentMechanism": { - "additionalProperties": false, - "description": "", - "properties": { - "mechanism": { - "type": "string" - }, - "treatment": { - "type": "string" - } - }, - "title": "TreatmentMechanism", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/composite_disease", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "contraindications": { - "description": "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.", - "items": { - "type": "string" - }, - "type": "array" - }, - "drugs": { - "description": "semicolon-separated list of named small molecule drugs", - "items": { - "type": "string" - }, - "type": "array" - }, - "main_disease": { - "description": "the name of the disease that is treated.", - "type": "string" - }, - "treatment_adverse_effects": { - "description": "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea", - "items": { - "$ref": "#/$defs/TreatmentAdverseEffect" - }, - "type": "array" - }, - "treatment_efficacies": { - "description": "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective", - "items": { - "$ref": "#/$defs/TreatmentEfficacy" - }, - "type": "array" - }, - "treatment_mechanisms": { - "description": "semicolon-separated list of treatment to asterisk-separated mechanism associations", - "items": { - "$ref": "#/$defs/TreatmentMechanism" - }, - "type": "array" - }, - "treatments": { - "description": "semicolon-separated list of therapies and treatments are indicated for treating the disease.", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "composite_disease", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/composite_disease/owl/composite_disease.owl.ttl b/projects/composite_disease/owl/composite_disease.owl.ttl deleted file mode 100644 index b9e698233..000000000 --- a/projects/composite_disease/owl/composite_disease.owl.ttl +++ /dev/null @@ -1,576 +0,0 @@ -@prefix IAO: . -@prefix composite_disease: . -@prefix linkml: . -@prefix owl: . -@prefix rdf: . -@prefix rdfs: . -@prefix skos: . -@prefix xsd: . - - a owl:Ontology ; - rdfs:label "composite_disease" ; - IAO:0000700 composite_disease:CompositeDisease, - , - , - , - , - , - , - ; - linkml:classes "{'CompositeDisease': ClassDefinition(name='CompositeDisease', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/CompositeDisease', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['compositeDisease__main_disease', 'compositeDisease__drugs', 'compositeDisease__treatments', 'compositeDisease__contraindications', 'compositeDisease__treatment_mechanisms', 'compositeDisease__treatment_efficacies', 'compositeDisease__treatment_adverse_effects'], slot_usage={}, attributes={'main_disease': SlotDefinition(name='main_disease', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the disease that is treated.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'drugs': SlotDefinition(name='drugs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of named small molecule drugs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Drug', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatments': SlotDefinition(name='treatments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.examples': Annotation(tag='prompt.examples', value='Imatinib, exercise, surgery', extensions={}, annotations={})}, description='semicolon-separated list of therapies and treatments are indicated for treating the disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'contraindications': SlotDefinition(name='contraindications', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.examples': Annotation(tag='prompt.examples', value='Beta-blockers, exercise, surgery', extensions={}, annotations={})}, description='semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_mechanisms': SlotDefinition(name='treatment_mechanisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to asterisk-separated mechanism associations', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentMechanism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_efficacies': SlotDefinition(name='treatment_efficacies', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentEfficacy', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_adverse_effects': SlotDefinition(name='treatment_adverse_effects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentAdverseEffect', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='composite_disease:CompositeDisease', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC'], definition_uri='http://w3id.org/ontogpt/composite_disease/Gene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, obo:sql:hgnc, bioportal:hgnc-nr', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='composite_disease:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Symptom': ClassDefinition(name='Symptom', id_prefixes=['HP'], definition_uri='http://w3id.org/ontogpt/composite_disease/Symptom', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hp', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='composite_disease:Symptom', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Disease': ClassDefinition(name='Disease', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/Disease', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:mondo', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='composite_disease:Disease', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AdverseEffect': ClassDefinition(name='AdverseEffect', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/AdverseEffect', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hp, sqlite:obo:ncit', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='composite_disease:AdverseEffect', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Treatment': ClassDefinition(name='Treatment', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/Treatment', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['NCITDrugType', 'NCITTreatmentType', 'NCITActivityType', 'MAXOTreatmentType', 'MESHTherapeuticType', 'CHEBIDrugType'], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='composite_disease:Treatment', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Mechanism': ClassDefinition(name='Mechanism', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/Mechanism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='composite_disease:Mechanism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Drug': ClassDefinition(name='Drug', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/Drug', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:chebi, sqlite:obo:drugbank', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='composite_disease:Drug', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TreatmentMechanism': ClassDefinition(name='TreatmentMechanism', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/TreatmentMechanism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['treatmentMechanism__treatment', 'treatmentMechanism__mechanism'], slot_usage={}, attributes={'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'mechanism': SlotDefinition(name='mechanism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Mechanism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='composite_disease:TreatmentMechanism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TreatmentAdverseEffect': ClassDefinition(name='TreatmentAdverseEffect', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/TreatmentAdverseEffect', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['treatmentAdverseEffect__treatment', 'treatmentAdverseEffect__adverse_effects'], slot_usage={}, attributes={'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'adverse_effects': SlotDefinition(name='adverse_effects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='AdverseEffect', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='composite_disease:TreatmentAdverseEffect', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TreatmentEfficacy': ClassDefinition(name='TreatmentEfficacy', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/TreatmentEfficacy', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['treatmentEfficacy__treatment', 'treatmentEfficacy__efficacy'], slot_usage={}, attributes={'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'efficacy': SlotDefinition(name='efficacy', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='composite_disease:TreatmentEfficacy', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NCITDrugType': EnumDefinition(name='NCITDrugType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/NCITDrugType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:ncit', source_nodes=['NCIT:C1908'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NCITTreatmentType': EnumDefinition(name='NCITTreatmentType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/NCITTreatmentType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:ncit', source_nodes=['NCIT:C25218'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NCITTActivityType': EnumDefinition(name='NCITTActivityType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/NCITTActivityType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:ncit', source_nodes=['NCIT:C43431'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'MAXOActionType': EnumDefinition(name='MAXOActionType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/MAXOActionType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:maxo', source_nodes=['MAXO:0000001'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'MESHTherapeuticType': EnumDefinition(name='MESHTherapeuticType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/MESHTherapeuticType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:mesh', source_nodes=['MESH:D013812'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'CHEBIDrugType': EnumDefinition(name='CHEBIDrugType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/composite_disease/CHEBIDrugType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/composite_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:chebi', source_nodes=['CHEBI:23888'], relationship_types=['rdfs:subClassOf', 'RO:0000087'], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/composite_disease" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -composite_disease:CHEBIDrugType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "CHEBIDrugType" ; - owl:unionOf [ rdf:rest () ] . - -composite_disease:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - composite_disease:annotators "gilda:, obo:sql:hgnc, bioportal:hgnc-nr" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -composite_disease:MAXOActionType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "MAXOActionType" ; - owl:unionOf [ rdf:rest () ] . - -composite_disease:MESHTherapeuticType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "MESHTherapeuticType" ; - owl:unionOf [ rdf:rest () ] . - -composite_disease:NCITDrugType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NCITDrugType" ; - owl:unionOf [ rdf:rest () ] . - -composite_disease:NCITTActivityType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NCITTActivityType" ; - owl:unionOf [ rdf:rest () ] . - -composite_disease:NCITTreatmentType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NCITTreatmentType" ; - owl:unionOf [ rdf:rest () ] . - -composite_disease:Symptom a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Symptom" ; - composite_disease:annotators "sqlite:obo:hp" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -composite_disease:CompositeDisease a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompositeDisease" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass composite_disease:Disease ; - owl:onProperty composite_disease:main_disease ], - [ a owl:Restriction ; - owl:allValuesFrom composite_disease:TreatmentMechanism ; - owl:onProperty composite_disease:treatment_mechanisms ], - [ a owl:Restriction ; - owl:allValuesFrom composite_disease:TreatmentAdverseEffect ; - owl:onProperty composite_disease:treatment_adverse_effects ], - [ a owl:Restriction ; - owl:allValuesFrom composite_disease:Treatment ; - owl:onProperty composite_disease:contraindications ], - [ a owl:Restriction ; - owl:allValuesFrom composite_disease:TreatmentEfficacy ; - owl:onProperty composite_disease:treatment_efficacies ], - [ a owl:Restriction ; - owl:allValuesFrom composite_disease:Treatment ; - owl:onProperty composite_disease:treatments ], - [ a owl:Restriction ; - owl:allValuesFrom composite_disease:Drug ; - owl:onProperty composite_disease:drugs ] ; - linkml:attributes "{'main_disease': SlotDefinition(name='main_disease', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the disease that is treated.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'drugs': SlotDefinition(name='drugs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of named small molecule drugs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Drug', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatments': SlotDefinition(name='treatments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.examples': Annotation(tag='prompt.examples', value='Imatinib, exercise, surgery', extensions={}, annotations={})}, description='semicolon-separated list of therapies and treatments are indicated for treating the disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'contraindications': SlotDefinition(name='contraindications', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.examples': Annotation(tag='prompt.examples', value='Beta-blockers, exercise, surgery', extensions={}, annotations={})}, description='semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_mechanisms': SlotDefinition(name='treatment_mechanisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to asterisk-separated mechanism associations', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentMechanism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_efficacies': SlotDefinition(name='treatment_efficacies', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentEfficacy', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_adverse_effects': SlotDefinition(name='treatment_adverse_effects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentAdverseEffect', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -composite_disease:adverse_effects a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "adverse_effects" ; - rdfs:range composite_disease:AdverseEffect . - -composite_disease:contraindications a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "contraindications" ; - composite_disease:prompt.examples "Beta-blockers, exercise, surgery" ; - rdfs:range composite_disease:Treatment ; - skos:definition "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects." . - -composite_disease:drugs a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "drugs" ; - rdfs:range composite_disease:Drug ; - skos:definition "semicolon-separated list of named small molecule drugs" . - -composite_disease:efficacy a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "efficacy" ; - rdfs:range linkml:String . - -composite_disease:main_disease a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "main_disease" ; - rdfs:range composite_disease:Disease ; - skos:definition "the name of the disease that is treated." . - -composite_disease:mechanism a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "mechanism" ; - rdfs:range composite_disease:Mechanism . - -composite_disease:treatment_adverse_effects a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatment_adverse_effects" ; - composite_disease:prompt.separator "*" ; - rdfs:range composite_disease:TreatmentAdverseEffect ; - skos:definition "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea" . - -composite_disease:treatment_efficacies a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatment_efficacies" ; - composite_disease:prompt.separator "*" ; - rdfs:range composite_disease:TreatmentEfficacy ; - skos:definition "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective" . - -composite_disease:treatment_mechanisms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatment_mechanisms" ; - composite_disease:prompt.separator "*" ; - rdfs:range composite_disease:TreatmentMechanism ; - skos:definition "semicolon-separated list of treatment to asterisk-separated mechanism associations" . - -composite_disease:treatments a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatments" ; - composite_disease:prompt.examples "Imatinib, exercise, surgery" ; - rdfs:range composite_disease:Treatment ; - skos:definition "semicolon-separated list of therapies and treatments are indicated for treating the disease." . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range ; - skos:definition "The complex objects extracted from the text" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range ; - skos:definition "Named entities extracted from the text" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - composite_disease:prompt.skip "true" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - composite_disease:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch . - - a , - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - - a , - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -composite_disease:AdverseEffect a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AdverseEffect" ; - composite_disease:annotators "sqlite:obo:hp, sqlite:obo:ncit" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -composite_disease:Disease a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Disease" ; - composite_disease:annotators "sqlite:obo:mondo" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -composite_disease:Drug a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Drug" ; - composite_disease:annotators "sqlite:obo:chebi, sqlite:obo:drugbank" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -composite_disease:Mechanism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Mechanism" ; - composite_disease:annotators "sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -composite_disease:TreatmentAdverseEffect a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TreatmentAdverseEffect" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass composite_disease:Treatment ; - owl:onProperty composite_disease:treatment ], - [ a owl:Restriction ; - owl:allValuesFrom composite_disease:AdverseEffect ; - owl:onProperty composite_disease:adverse_effects ], - ; - linkml:attributes "{'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'adverse_effects': SlotDefinition(name='adverse_effects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='AdverseEffect', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -composite_disease:TreatmentEfficacy a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TreatmentEfficacy" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass composite_disease:Treatment ; - owl:onProperty composite_disease:treatment ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty composite_disease:efficacy ], - ; - linkml:attributes "{'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'efficacy': SlotDefinition(name='efficacy', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -composite_disease:TreatmentMechanism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TreatmentMechanism" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass composite_disease:Treatment ; - owl:onProperty composite_disease:treatment ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass composite_disease:Mechanism ; - owl:onProperty composite_disease:mechanism ], - ; - linkml:attributes "{'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'mechanism': SlotDefinition(name='mechanism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Mechanism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - - a , - owl:Class ; - rdfs:label "NOT_MENTIONED" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - - a owl:ObjectProperty, - linkml:SlotDefinition . - -composite_disease:treatment a owl:ObjectProperty, - linkml:SlotDefinition . - - a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( ) ; - linkml:permissible_values , - , - . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -composite_disease:Treatment a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Treatment" ; - composite_disease:annotators "sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi" ; - rdfs:subClassOf ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - - a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/composite_disease/prefixmap/composite_disease.yaml b/projects/composite_disease/prefixmap/composite_disease.yaml deleted file mode 100644 index 2a737b3b7..000000000 --- a/projects/composite_disease/prefixmap/composite_disease.yaml +++ /dev/null @@ -1,37 +0,0 @@ -{ - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "HP": "http://example.org/UNKNOWN/HP/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "composite_disease": "http://w3id.org/ontogpt/composite_disease/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/composite_disease/protobuf/composite_disease.proto b/projects/composite_disease/protobuf/composite_disease.proto deleted file mode 100644 index 0a2324473..000000000 --- a/projects/composite_disease/protobuf/composite_disease.proto +++ /dev/null @@ -1,95 +0,0 @@ -message AdverseEffect - { - string id = 0 - string label = 0 - } -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message CompositeDisease - { - disease mainDisease = 0 - repeated drug drugs = 0 - repeated treatment treatments = 0 - repeated treatment contraindications = 0 - repeated treatmentMechanism treatmentMechanisms = 0 - repeated treatmentEfficacy treatmentEfficacies = 0 - repeated treatmentAdverseEffect treatmentAdverseEffects = 0 - } -message Disease - { - string id = 0 - string label = 0 - } -message Drug - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -message Mechanism - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message Symptom - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Treatment - { - string id = 0 - string label = 0 - } -message TreatmentAdverseEffect - { - treatment treatment = 0 - repeated adverseEffect adverseEffects = 0 - } -message TreatmentEfficacy - { - treatment treatment = 0 - string efficacy = 0 - } -message TreatmentMechanism - { - treatment treatment = 0 - mechanism mechanism = 0 - } diff --git a/projects/composite_disease/shacl/composite_disease.shacl.ttl b/projects/composite_disease/shacl/composite_disease.shacl.ttl deleted file mode 100644 index 8053d0fd7..000000000 --- a/projects/composite_disease/shacl/composite_disease.shacl.ttl +++ /dev/null @@ -1,345 +0,0 @@ -@prefix composite_disease: . -@prefix linkml: . -@prefix rdf: . -@prefix sh: . -@prefix xsd: . - -composite_disease:CompositeDisease a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class composite_disease:TreatmentMechanism ; - sh:description "semicolon-separated list of treatment to asterisk-separated mechanism associations" ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path composite_disease:treatment_mechanisms ], - [ sh:class composite_disease:Treatment ; - sh:description "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path composite_disease:contraindications ], - [ sh:class composite_disease:Disease ; - sh:description "the name of the disease that is treated." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path composite_disease:main_disease ], - [ sh:class composite_disease:TreatmentEfficacy ; - sh:description "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective" ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path composite_disease:treatment_efficacies ], - [ sh:class composite_disease:Drug ; - sh:description "semicolon-separated list of named small molecule drugs" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path composite_disease:drugs ], - [ sh:class composite_disease:TreatmentAdverseEffect ; - sh:description "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path composite_disease:treatment_adverse_effects ], - [ sh:class composite_disease:Treatment ; - sh:description "semicolon-separated list of therapies and treatments are indicated for treating the disease." ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path composite_disease:treatments ] ; - sh:targetClass composite_disease:CompositeDisease . - -composite_disease:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass composite_disease:Gene . - -composite_disease:Symptom a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass composite_disease:Symptom . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path ], - [ sh:class ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path ] ; - sh:targetClass . - -composite_disease:AdverseEffect a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass composite_disease:AdverseEffect . - -composite_disease:Disease a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass composite_disease:Disease . - -composite_disease:Drug a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass composite_disease:Drug . - -composite_disease:Mechanism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass composite_disease:Mechanism . - -composite_disease:TreatmentAdverseEffect a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class composite_disease:AdverseEffect ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path composite_disease:adverse_effects ], - [ sh:class composite_disease:Treatment ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path composite_disease:treatment ] ; - sh:targetClass composite_disease:TreatmentAdverseEffect . - -composite_disease:TreatmentEfficacy a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class composite_disease:Treatment ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path composite_disease:treatment ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path composite_disease:efficacy ] ; - sh:targetClass composite_disease:TreatmentEfficacy . - -composite_disease:TreatmentMechanism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class composite_disease:Treatment ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path composite_disease:treatment ], - [ sh:class composite_disease:Mechanism ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path composite_disease:mechanism ] ; - sh:targetClass composite_disease:TreatmentMechanism . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - - a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path ], - [ sh:class ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path ], - [ sh:class ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path ], - [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path ], - [ sh:class ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path ] ; - sh:targetClass . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - - a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ] ; - sh:targetClass . - -composite_disease:Treatment a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ] ; - sh:targetClass composite_disease:Treatment . - diff --git a/projects/composite_disease/shex/composite_disease.shex b/projects/composite_disease/shex/composite_disease.shex deleted file mode 100644 index f59e6d75b..000000000 --- a/projects/composite_disease/shex/composite_disease.shex +++ /dev/null @@ -1,235 +0,0 @@ -BASE -PREFIX rdf: -PREFIX xsd: -PREFIX linkml: -PREFIX core: -PREFIX rdfs1: - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - - CLOSED { - ( $ ( @ ? ; - @ * ; - @ * ; - @ * ; - @ * ; - @ * ; - @ * - ) ; - rdf:type [ ] ? - ) -} - -core:CompoundExpression ( - @ OR @ OR @ OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - -core:NamedEntity ( - @ OR @ OR @ OR @ OR @ OR @core:RelationshipType OR @ OR @ -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - - CLOSED { - ( $ ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ ] - ) -} - - CLOSED { - ( $ ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - @ ? ; - @ * - ) ; - rdf:type [ ] ? - ) -} - - CLOSED { - ( $ ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - @ ? ; - @linkml:String ? - ) ; - rdf:type [ ] ? - ) -} - - CLOSED { - ( $ ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - @ ? ; - @ ? - ) ; - rdf:type [ ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/composite_disease/sqlschema/composite_disease.sql b/projects/composite_disease/sqlschema/composite_disease.sql deleted file mode 100644 index 845d50f11..000000000 --- a/projects/composite_disease/sqlschema/composite_disease.sql +++ /dev/null @@ -1,116 +0,0 @@ - - -CREATE TABLE "AdverseEffect" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Disease" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Drug" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Mechanism" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Symptom" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Treatment" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "CompositeDisease" ( - main_disease TEXT, - drugs TEXT, - treatments TEXT, - contraindications TEXT, - treatment_mechanisms TEXT, - treatment_efficacies TEXT, - treatment_adverse_effects TEXT, - PRIMARY KEY (main_disease, drugs, treatments, contraindications, treatment_mechanisms, treatment_efficacies, treatment_adverse_effects), - FOREIGN KEY(main_disease) REFERENCES "Disease" (id) -); - -CREATE TABLE "TreatmentAdverseEffect" ( - treatment TEXT, - adverse_effects TEXT, - PRIMARY KEY (treatment, adverse_effects), - FOREIGN KEY(treatment) REFERENCES "Treatment" (id) -); - -CREATE TABLE "TreatmentEfficacy" ( - treatment TEXT, - efficacy TEXT, - PRIMARY KEY (treatment, efficacy), - FOREIGN KEY(treatment) REFERENCES "Treatment" (id) -); - -CREATE TABLE "TreatmentMechanism" ( - treatment TEXT, - mechanism TEXT, - PRIMARY KEY (treatment, mechanism), - FOREIGN KEY(treatment) REFERENCES "Treatment" (id), - FOREIGN KEY(mechanism) REFERENCES "Mechanism" (id) -); diff --git a/projects/core/core.py b/projects/core/core.py deleted file mode 100644 index 42c1e37f7..000000000 --- a/projects/core/core.py +++ /dev/null @@ -1,362 +0,0 @@ -# Auto generated from core.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:52:11 -# Schema: core -# -# id: http://w3id.org/ontogpt/core -# description: Core upper level -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -NCIT = CurieNamespace('NCIT', 'http://purl.obolibrary.org/obo/NCIT_') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = CORE - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = CORE.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = CORE.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = CORE.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = CORE.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = CORE.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = CORE.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = CORE.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = CORE.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=CORE.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=CORE.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=CORE.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=CORE.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=CORE.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=CORE.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=CORE.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=CORE.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=CORE.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=CORE.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=CORE.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=CORE.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=CORE.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=CORE.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=CORE.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=CORE.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=CORE.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=CORE.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=CORE.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=CORE.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=CORE.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=CORE.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=CORE.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=CORE.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=CORE.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/core/docs/AnnotatorResult.md b/projects/core/docs/AnnotatorResult.md deleted file mode 100644 index 64a2e261b..000000000 --- a/projects/core/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [core:AnnotatorResult](http://w3id.org/ontogpt/core/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) 0..1 - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) 0..1 - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) 0..1 - * Range: [String](types/String.md) diff --git a/projects/core/docs/Any.md b/projects/core/docs/Any.md deleted file mode 100644 index 109c12ca2..000000000 --- a/projects/core/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [core:Any](http://w3id.org/ontogpt/core/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* 0..1 **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* 0..\* **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/core/docs/CompoundExpression.md b/projects/core/docs/CompoundExpression.md deleted file mode 100644 index 2f73ec8dd..000000000 --- a/projects/core/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [core:CompoundExpression](http://w3id.org/ontogpt/core/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/core/docs/ExtractionResult.md b/projects/core/docs/ExtractionResult.md deleted file mode 100644 index dcb9d4665..000000000 --- a/projects/core/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [core:ExtractionResult](http://w3id.org/ontogpt/core/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]0..1 - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) 0..1 - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) 0..1 - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) 0..1 - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) 0..1 - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) 0..1 - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) 0..\* - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/core/docs/NamedEntity.md b/projects/core/docs/NamedEntity.md deleted file mode 100644 index 356e8abf6..000000000 --- a/projects/core/docs/NamedEntity.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [core:NamedEntity](http://w3id.org/ontogpt/core/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[Triple]) - -## Children - - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* 0..1 **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* 0..1 **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/core/docs/NullDataOptions.md b/projects/core/docs/NullDataOptions.md deleted file mode 100644 index fae7f8f08..000000000 --- a/projects/core/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [core:NullDataOptions](http://w3id.org/ontogpt/core/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/core/docs/Publication.md b/projects/core/docs/Publication.md deleted file mode 100644 index 0a70ed378..000000000 --- a/projects/core/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [core:Publication](http://w3id.org/ontogpt/core/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* 0..1 **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) 0..1 - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) 0..1 - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) 0..1 - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) 0..1 - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) 0..1 - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/core/docs/RelationshipType.md b/projects/core/docs/RelationshipType.md deleted file mode 100644 index 83361ef96..000000000 --- a/projects/core/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [core:RelationshipType](http://w3id.org/ontogpt/core/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* 0..1 **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) 1..1 - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) 0..1 - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/core/docs/TextWithTriples.md b/projects/core/docs/TextWithTriples.md deleted file mode 100644 index 4b9147f9d..000000000 --- a/projects/core/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [core:TextWithTriples](http://w3id.org/ontogpt/core/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]0..1 - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) 0..\* - * Range: [Triple](Triple.md) diff --git a/projects/core/docs/Triple.md b/projects/core/docs/Triple.md deleted file mode 100644 index 70645a204..000000000 --- a/projects/core/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [core:Triple](http://w3id.org/ontogpt/core/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity][Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity][Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* 0..\* **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) 0..1 - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) 0..1 - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) 0..1 - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) 0..1 - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) 0..1 - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) 0..1 - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/core/docs/annotatorResult__object_id.md b/projects/core/docs/annotatorResult__object_id.md deleted file mode 100644 index 43da8c67b..000000000 --- a/projects/core/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [core:annotatorResult__object_id](http://w3id.org/ontogpt/core/annotatorResult__object_id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/core/docs/annotatorResult__object_text.md b/projects/core/docs/annotatorResult__object_text.md deleted file mode 100644 index fd16826f3..000000000 --- a/projects/core/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [core:annotatorResult__object_text](http://w3id.org/ontogpt/core/annotatorResult__object_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/core/docs/annotatorResult__subject_text.md b/projects/core/docs/annotatorResult__subject_text.md deleted file mode 100644 index 6f954fd44..000000000 --- a/projects/core/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [core:annotatorResult__subject_text](http://w3id.org/ontogpt/core/annotatorResult__subject_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/core/docs/core.md b/projects/core/docs/core.md deleted file mode 100644 index 325d6b2ff..000000000 --- a/projects/core/docs/core.md +++ /dev/null @@ -1,103 +0,0 @@ - -# core - - -**metamodel version:** 1.7.0 - -**version:** None - - -Core upper level - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/core/docs/extractionResult__extracted_object.md b/projects/core/docs/extractionResult__extracted_object.md deleted file mode 100644 index 4df7da90c..000000000 --- a/projects/core/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [core:extractionResult__extracted_object](http://w3id.org/ontogpt/core/extractionResult__extracted_object) - - -## Domain and Range - -None → 0..1 [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/core/docs/extractionResult__input_id.md b/projects/core/docs/extractionResult__input_id.md deleted file mode 100644 index 06b56bf83..000000000 --- a/projects/core/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [core:extractionResult__input_id](http://w3id.org/ontogpt/core/extractionResult__input_id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/core/docs/extractionResult__input_text.md b/projects/core/docs/extractionResult__input_text.md deleted file mode 100644 index 12569eae8..000000000 --- a/projects/core/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [core:extractionResult__input_text](http://w3id.org/ontogpt/core/extractionResult__input_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/core/docs/extractionResult__input_title.md b/projects/core/docs/extractionResult__input_title.md deleted file mode 100644 index 07700cc95..000000000 --- a/projects/core/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [core:extractionResult__input_title](http://w3id.org/ontogpt/core/extractionResult__input_title) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/core/docs/extractionResult__named_entities.md b/projects/core/docs/extractionResult__named_entities.md deleted file mode 100644 index 830aeca3f..000000000 --- a/projects/core/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [core:extractionResult__named_entities](http://w3id.org/ontogpt/core/extractionResult__named_entities) - - -## Domain and Range - -None → 0..\* [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/core/docs/extractionResult__prompt.md b/projects/core/docs/extractionResult__prompt.md deleted file mode 100644 index 04bf5d29b..000000000 --- a/projects/core/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [core:extractionResult__prompt](http://w3id.org/ontogpt/core/extractionResult__prompt) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/core/docs/extractionResult__raw_completion_output.md b/projects/core/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 6f86f7266..000000000 --- a/projects/core/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [core:extractionResult__raw_completion_output](http://w3id.org/ontogpt/core/extractionResult__raw_completion_output) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/core/docs/namedEntity__id.md b/projects/core/docs/namedEntity__id.md deleted file mode 100644 index c4285c132..000000000 --- a/projects/core/docs/namedEntity__id.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [core:namedEntity__id](http://w3id.org/ontogpt/core/namedEntity__id) - - -## Domain and Range - -None → 1..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/core/docs/namedEntity__label.md b/projects/core/docs/namedEntity__label.md deleted file mode 100644 index 8310a070f..000000000 --- a/projects/core/docs/namedEntity__label.md +++ /dev/null @@ -1,31 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [core:namedEntity__label](http://w3id.org/ontogpt/core/namedEntity__label) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/core/docs/publication__abstract.md b/projects/core/docs/publication__abstract.md deleted file mode 100644 index 6345cf85f..000000000 --- a/projects/core/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [core:publication__abstract](http://w3id.org/ontogpt/core/publication__abstract) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/core/docs/publication__combined_text.md b/projects/core/docs/publication__combined_text.md deleted file mode 100644 index fc0082cbe..000000000 --- a/projects/core/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [core:publication__combined_text](http://w3id.org/ontogpt/core/publication__combined_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/core/docs/publication__full_text.md b/projects/core/docs/publication__full_text.md deleted file mode 100644 index 60df5cc89..000000000 --- a/projects/core/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [core:publication__full_text](http://w3id.org/ontogpt/core/publication__full_text) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/core/docs/publication__id.md b/projects/core/docs/publication__id.md deleted file mode 100644 index 9cc7a1bec..000000000 --- a/projects/core/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [core:publication__id](http://w3id.org/ontogpt/core/publication__id) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/core/docs/publication__title.md b/projects/core/docs/publication__title.md deleted file mode 100644 index 01cf66963..000000000 --- a/projects/core/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [core:publication__title](http://w3id.org/ontogpt/core/publication__title) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/core/docs/textWithTriples__publication.md b/projects/core/docs/textWithTriples__publication.md deleted file mode 100644 index 3d3b57bd1..000000000 --- a/projects/core/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [core:textWithTriples__publication](http://w3id.org/ontogpt/core/textWithTriples__publication) - - -## Domain and Range - -None → 0..1 [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/core/docs/textWithTriples__triples.md b/projects/core/docs/textWithTriples__triples.md deleted file mode 100644 index bf9ab7a93..000000000 --- a/projects/core/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [core:textWithTriples__triples](http://w3id.org/ontogpt/core/textWithTriples__triples) - - -## Domain and Range - -None → 0..\* [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/core/docs/triple__object.md b/projects/core/docs/triple__object.md deleted file mode 100644 index 906a3f8c9..000000000 --- a/projects/core/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [core:triple__object](http://w3id.org/ontogpt/core/triple__object) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/core/docs/triple__object_qualifier.md b/projects/core/docs/triple__object_qualifier.md deleted file mode 100644 index e599434ac..000000000 --- a/projects/core/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [core:triple__object_qualifier](http://w3id.org/ontogpt/core/triple__object_qualifier) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/core/docs/triple__predicate.md b/projects/core/docs/triple__predicate.md deleted file mode 100644 index 2a475a200..000000000 --- a/projects/core/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [core:triple__predicate](http://w3id.org/ontogpt/core/triple__predicate) - - -## Domain and Range - -None → 0..1 [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/core/docs/triple__qualifier.md b/projects/core/docs/triple__qualifier.md deleted file mode 100644 index 5488b6a06..000000000 --- a/projects/core/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [core:triple__qualifier](http://w3id.org/ontogpt/core/triple__qualifier) - - -## Domain and Range - -None → 0..1 [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/core/docs/triple__subject.md b/projects/core/docs/triple__subject.md deleted file mode 100644 index d054483fb..000000000 --- a/projects/core/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [core:triple__subject](http://w3id.org/ontogpt/core/triple__subject) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/core/docs/triple__subject_qualifier.md b/projects/core/docs/triple__subject_qualifier.md deleted file mode 100644 index 628145a99..000000000 --- a/projects/core/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [core:triple__subject_qualifier](http://w3id.org/ontogpt/core/triple__subject_qualifier) - - -## Domain and Range - -None → 0..1 [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/core/docs/types/Boolean.md b/projects/core/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/core/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/core/docs/types/Curie.md b/projects/core/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/core/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/core/docs/types/Date.md b/projects/core/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/core/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/core/docs/types/DateOrDatetime.md b/projects/core/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/core/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/core/docs/types/Datetime.md b/projects/core/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/core/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/core/docs/types/Decimal.md b/projects/core/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/core/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/core/docs/types/Double.md b/projects/core/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/core/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/core/docs/types/Float.md b/projects/core/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/core/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/core/docs/types/Integer.md b/projects/core/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/core/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/core/docs/types/Jsonpath.md b/projects/core/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/core/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/core/docs/types/Jsonpointer.md b/projects/core/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/core/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/core/docs/types/Ncname.md b/projects/core/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/core/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/core/docs/types/Nodeidentifier.md b/projects/core/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/core/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/core/docs/types/Objectidentifier.md b/projects/core/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/core/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/core/docs/types/Sparqlpath.md b/projects/core/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/core/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/core/docs/types/String.md b/projects/core/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/core/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/core/docs/types/Time.md b/projects/core/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/core/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/core/docs/types/Uri.md b/projects/core/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/core/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/core/docs/types/Uriorcurie.md b/projects/core/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/core/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/core/excel/core.xlsx b/projects/core/excel/core.xlsx deleted file mode 100644 index 29894fd7ae2f07d26104d9d6298eefaaec16c9ab..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 7279 zcmZ`;1yodByB@k@XlVol>F(~30VIT>OF|l?q(MNsLAsGf>F(~38cG3a=|;Gt-v9c` z{l1xX&R(V?#c+EE$$jY<*)sEcODxZK=;WA3jhHBd%q@j zj%GhMJQ6!*)y0M$Y+!bo(Jz0F6?gqb|IxF@*{U_>yNZjrAH9BJ&Wy4 zzW{<0xHrS14JCKS1u<7nILI=V|->dJAvEd{I*6T5=y~HEP#E z^)y$m1D>f+vp<@bBq{(b20$T@iuHp&; 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rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/core/jsonld/core.context.jsonld b/projects/core/jsonld/core.context.jsonld deleted file mode 100644 index 051442c6c..000000000 --- a/projects/core/jsonld/core.context.jsonld +++ /dev/null @@ -1,56 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:52:04", - "source": "core.yaml" - }, - "@context": { - "NCIT": { - "@id": "http://purl.obolibrary.org/obo/NCIT_", - "@prefix": true - }, - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/core/", - "extracted_object": { - "@type": "@id" - }, - "named_entities": { - "@type": "@id" - }, - "id": "@id", - "label": { - "@id": "rdfs:label" - }, - "publication": { - "@type": "@id" - }, - "triples": { - "@type": "@id" - }, - "object": { - "@type": "@id" - }, - "object_qualifier": { - "@type": "@id" - }, - "predicate": { - "@type": "@id" - }, - "subject": { - "@type": "@id" - }, - "subject_qualifier": { - "@type": "@id" - }, - "Any": { - "@id": "linkml:Any" - } - } -} diff --git a/projects/core/jsonld/core.jsonld b/projects/core/jsonld/core.jsonld deleted file mode 100644 index d0afe9a72..000000000 --- a/projects/core/jsonld/core.jsonld +++ /dev/null @@ -1,977 +0,0 @@ -{ - "name": "core", - "description": "Core upper level", - "title": "AI core Template", - "id": "http://w3id.org/ontogpt/core", - "imports": [ - "linkml:types" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "core", - "prefix_reference": "http://w3id.org/ontogpt/core/" - }, - { - "prefix_prefix": "NCIT", - "prefix_reference": "http://purl.obolibrary.org/obo/NCIT_" - }, - { - "prefix_prefix": "RO", - "prefix_reference": "http://purl.obolibrary.org/obo/RO_" - } - ], - "default_prefix": "core", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "core.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 3446, - "generation_date": "2023-08-07T10:52:05", - "@type": "SchemaDefinition", - "@context": [ - "projects/core/jsonld/core.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/core/" - } - ] -} diff --git a/projects/core/jsonschema/core.schema.json b/projects/core/jsonschema/core.schema.json deleted file mode 100644 index a51b370dd..000000000 --- a/projects/core/jsonschema/core.schema.json +++ /dev/null @@ -1,141 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/core", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "core", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/core/owl/core.owl.ttl b/projects/core/owl/core.owl.ttl deleted file mode 100644 index e9faa8a12..000000000 --- a/projects/core/owl/core.owl.ttl +++ /dev/null @@ -1,353 +0,0 @@ -@prefix IAO: . -@prefix NCIT: . -@prefix core: . -@prefix linkml: . -@prefix owl: . -@prefix rdf: . -@prefix rdfs: . -@prefix skos: . -@prefix xsd: . - - a owl:Ontology ; - rdfs:label "core" ; - IAO:0000700 core:AnnotatorResult, - core:Any, - core:CompoundExpression, - core:ExtractionResult, - core:NamedEntity, - core:Publication, - core:TextWithTriples ; - linkml:classes "{'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/core" ; - linkml:imports "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -core:AnnotatorResult a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:object_text ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:subject_text ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:object_id ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -core:ExtractionResult a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:prompt ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:input_title ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:input_text ], - [ a owl:Restriction ; - owl:allValuesFrom core:Any ; - owl:onProperty core:named_entities ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:input_id ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:raw_completion_output ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:Any ; - owl:onProperty core:extracted_object ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -core:TextWithTriples a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom core:Triple ; - owl:onProperty core:triples ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:Publication ; - owl:onProperty core:publication ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -core:abstract a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -core:combined_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -core:extracted_object a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range core:Any ; - skos:definition "The complex objects extracted from the text" . - -core:full_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -core:input_id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -core:input_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -core:input_title a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -core:named_entities a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range core:Any ; - skos:definition "Named entities extracted from the text" . - -core:object a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range core:NamedEntity . - -core:object_id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -core:object_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range core:NamedEntity ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -core:object_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -core:predicate a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range core:RelationshipType . - -core:prompt a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -core:publication a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - core:prompt.skip "true" ; - rdfs:range core:Publication . - -core:qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -core:raw_completion_output a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -core:subject a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range core:NamedEntity . - -core:subject_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range core:NamedEntity ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -core:subject_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -core:title a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -core:triples a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range core:Triple . - - a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - core:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch . - -NCIT:C149701 a core:NullDataOptions, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -NCIT:C18902 a core:NullDataOptions, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -core:CompoundExpression a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - - a core:NullDataOptions, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -core:RelationshipType a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf core:NamedEntity ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -core:Triple a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty core:subject_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty core:object_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty core:object ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:RelationshipType ; - owl:onProperty core:predicate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty core:subject ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:qualifier ], - core:CompoundExpression ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -core:id a owl:ObjectProperty, - linkml:SlotDefinition . - -core:NullDataOptions a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( NCIT:C149701 NCIT:C18902 ) ; - linkml:permissible_values NCIT:C149701, - NCIT:C18902, - . - -core:Publication a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:abstract ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:id ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:title ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:combined_text ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:full_text ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -core:Any a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -core:NamedEntity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty core:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/core/prefixmap/core.yaml b/projects/core/prefixmap/core.yaml deleted file mode 100644 index 5bb6968d5..000000000 --- a/projects/core/prefixmap/core.yaml +++ /dev/null @@ -1,11 +0,0 @@ -{ - "NCIT": "http://purl.obolibrary.org/obo/NCIT_", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "Any": { - "@id": "linkml:Any" - } -} diff --git a/projects/core/protobuf/core.proto b/projects/core/protobuf/core.proto deleted file mode 100644 index c3cc6b1ba..000000000 --- a/projects/core/protobuf/core.proto +++ /dev/null @@ -1,35 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/core/shacl/core.shacl.ttl b/projects/core/shacl/core.shacl.ttl deleted file mode 100644 index 9ee4c542b..000000000 --- a/projects/core/shacl/core.shacl.ttl +++ /dev/null @@ -1,164 +0,0 @@ -@prefix core: . -@prefix linkml: . -@prefix rdf: . -@prefix sh: . -@prefix xsd: . - -core:AnnotatorResult a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path core:object_id ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path core:object_text ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path core:subject_text ] ; - sh:targetClass core:AnnotatorResult . - -core:CompoundExpression a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass core:CompoundExpression . - -core:ExtractionResult a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path core:input_title ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path core:input_id ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path core:named_entities ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path core:input_text ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path core:extracted_object ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path core:raw_completion_output ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path core:prompt ] ; - sh:targetClass core:ExtractionResult . - -core:TextWithTriples a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class core:Triple ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path core:triples ], - [ sh:class core:Publication ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path core:publication ] ; - sh:targetClass core:TextWithTriples . - -core:Publication a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path core:title ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path core:abstract ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path core:full_text ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path core:combined_text ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path core:id ] ; - sh:targetClass core:Publication . - -core:RelationshipType a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path core:id ] ; - sh:targetClass core:RelationshipType . - -core:Triple a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class core:NamedEntity ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path core:subject_qualifier ], - [ sh:class core:RelationshipType ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path core:predicate ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path core:qualifier ], - [ sh:class core:NamedEntity ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path core:object_qualifier ], - [ sh:class core:NamedEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path core:subject ], - [ sh:class core:NamedEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path core:object ] ; - sh:targetClass core:Triple . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -core:NamedEntity a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path core:id ] ; - sh:targetClass core:NamedEntity . - diff --git a/projects/core/shex/core.shex b/projects/core/shex/core.shex deleted file mode 100644 index 35be31fb3..000000000 --- a/projects/core/shex/core.shex +++ /dev/null @@ -1,131 +0,0 @@ -BASE -PREFIX rdf: -PREFIX xsd: -PREFIX linkml: -PREFIX rdfs1: - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - - CLOSED { - ( $ ( @linkml:String ? ; - @linkml:String ? ; - @linkml:String ? - ) ; - rdf:type [ ] ? - ) -} - - CLOSED { - ( $ rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - - ( - { - ( $ rdf:type . * ; - rdf:type [ ] ? - ) - } OR @ -) - - CLOSED { - ( $ ( @linkml:String ? ; - @linkml:String ? ; - @linkml:String ? ; - @linkml:String ? ; - @linkml:String ? ; - @ ? ; - @ * - ) ; - rdf:type [ ] ? - ) -} - - ( - { - ( $ rdfs1:label @linkml:String ? ; - rdf:type [ ] - ) - } OR @ -) - - CLOSED { - ( $ ( @linkml:String ? ; - @linkml:String ? ; - <abstract> @linkml:String ? ; - <combined_text> @linkml:String ? ; - <full_text> @linkml:String ? - ) ; - rdf:type [ <Publication> ] ? - ) -} - -<RelationshipType> CLOSED { - ( $<RelationshipType_tes> ( &<NamedEntity_tes> ; - rdf:type [ <NamedEntity> ] ? - ) ; - rdf:type [ <RelationshipType> ] - ) -} - -<TextWithTriples> CLOSED { - ( $<TextWithTriples_tes> ( <publication> @<Publication> ? ; - <triples> @<Triple> * - ) ; - rdf:type [ <TextWithTriples> ] ? - ) -} - -<Triple> { - ( $<Triple_tes> ( &<CompoundExpression_tes> ; - rdf:type [ <CompoundExpression> ] ? ; - <subject> @<NamedEntity> ? ; - <predicate> @<RelationshipType> ? ; - <object> @<NamedEntity> ? ; - <qualifier> @linkml:String ? ; - <subject_qualifier> @<NamedEntity> ? ; - <object_qualifier> @<NamedEntity> ? - ) ; - rdf:type [ <Triple> ] ? - ) -} - - diff --git a/projects/core/sqlschema/core.sql b/projects/core/sqlschema/core.sql deleted file mode 100644 index 0d5e7d23b..000000000 --- a/projects/core/sqlschema/core.sql +++ /dev/null @@ -1,40 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); diff --git a/projects/ctd/ctd.py b/projects/ctd/ctd.py deleted file mode 100644 index 9fa39d8ce..000000000 --- a/projects/ctd/ctd.py +++ /dev/null @@ -1,537 +0,0 @@ -# Auto generated from ctd.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:52:24 -# Schema: ctd -# -# id: http://w3id.org/ontogpt/ctd -# description: A template for Chemical to Disease associations. This template is intended to represent -# associations between chemicals and diseases, and for evaluating Semantic Llama against BioCreative -# V Chemical Disease Relation (CDR) Task (BC5CDR). -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -MESH = CurieNamespace('MESH', 'http://example.org/UNKNOWN/MESH/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -DRUG = CurieNamespace('drug', 'http://w3id.org/ontogpt/drug/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = DRUG - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class DiseaseId(NamedEntityId): - pass - - -class ChemicalId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -class ChemicalToDiseasePredicateId(RelationshipTypeId): - pass - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = DRUG.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = DRUG.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Disease(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.Disease - class_class_curie: ClassVar[str] = "drug:Disease" - class_name: ClassVar[str] = "Disease" - class_model_uri: ClassVar[URIRef] = DRUG.Disease - - id: Union[str, DiseaseId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiseaseId): - self.id = DiseaseId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Chemical(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.Chemical - class_class_curie: ClassVar[str] = "drug:Chemical" - class_name: ClassVar[str] = "Chemical" - class_model_uri: ClassVar[URIRef] = DRUG.Chemical - - id: Union[str, ChemicalId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalId): - self.id = ChemicalId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = DRUG.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = DRUG.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalToDiseaseRelationship(Triple): - """ - A triple where the subject is a chemical and the object is a disease. - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.ChemicalToDiseaseRelationship - class_class_curie: ClassVar[str] = "drug:ChemicalToDiseaseRelationship" - class_name: ClassVar[str] = "ChemicalToDiseaseRelationship" - class_model_uri: ClassVar[URIRef] = DRUG.ChemicalToDiseaseRelationship - - subject: Optional[Union[str, ChemicalId]] = None - object: Optional[Union[str, DiseaseId]] = None - predicate: Optional[Union[str, ChemicalToDiseasePredicateId]] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, ChemicalId): - self.subject = ChemicalId(self.subject) - - if self.object is not None and not isinstance(self.object, DiseaseId): - self.object = DiseaseId(self.object) - - if self.predicate is not None and not isinstance(self.predicate, ChemicalToDiseasePredicateId): - self.predicate = ChemicalToDiseasePredicateId(self.predicate) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = DRUG.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalToDiseaseDocument(TextWithTriples): - """ - A document that contains chemical to disease relations. - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.ChemicalToDiseaseDocument - class_class_curie: ClassVar[str] = "drug:ChemicalToDiseaseDocument" - class_name: ClassVar[str] = "ChemicalToDiseaseDocument" - class_model_uri: ClassVar[URIRef] = DRUG.ChemicalToDiseaseDocument - - triples: Optional[Union[Union[dict, "ChemicalToDiseaseRelationship"], List[Union[dict, "ChemicalToDiseaseRelationship"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, ChemicalToDiseaseRelationship) else ChemicalToDiseaseRelationship(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = DRUG.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalToDiseasePredicate(RelationshipType): - """ - A predicate for chemical to disease relationships - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.ChemicalToDiseasePredicate - class_class_curie: ClassVar[str] = "drug:ChemicalToDiseasePredicate" - class_name: ClassVar[str] = "ChemicalToDiseasePredicate" - class_model_uri: ClassVar[URIRef] = DRUG.ChemicalToDiseasePredicate - - id: Union[str, ChemicalToDiseasePredicateId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalToDiseasePredicateId): - self.id = ChemicalToDiseasePredicateId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = DRUG.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = DRUG.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class MeshChemicalIdentifier(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="MeshChemicalIdentifier", - ) - -class MeshDiseaseIdentifier(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="MeshDiseaseIdentifier", - ) - -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=DRUG.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=DRUG.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=DRUG.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=DRUG.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=DRUG.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=DRUG.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=DRUG.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=DRUG.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=DRUG.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=DRUG.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=DRUG.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=DRUG.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=DRUG.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=DRUG.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=DRUG.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=DRUG.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=DRUG.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=DRUG.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=DRUG.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=DRUG.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=DRUG.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=DRUG.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=DRUG.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=DRUG.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=DRUG.annotatorResult__object_text, domain=None, range=Optional[str]) - -slots.ChemicalToDiseaseDocument_triples = Slot(uri=DRUG.triples, name="ChemicalToDiseaseDocument_triples", curie=DRUG.curie('triples'), - model_uri=DRUG.ChemicalToDiseaseDocument_triples, domain=ChemicalToDiseaseDocument, range=Optional[Union[Union[dict, "ChemicalToDiseaseRelationship"], List[Union[dict, "ChemicalToDiseaseRelationship"]]]]) - -slots.ChemicalToDiseaseRelationship_subject = Slot(uri=DRUG.subject, name="ChemicalToDiseaseRelationship_subject", curie=DRUG.curie('subject'), - model_uri=DRUG.ChemicalToDiseaseRelationship_subject, domain=ChemicalToDiseaseRelationship, range=Optional[Union[str, ChemicalId]]) - -slots.ChemicalToDiseaseRelationship_object = Slot(uri=DRUG.object, name="ChemicalToDiseaseRelationship_object", curie=DRUG.curie('object'), - model_uri=DRUG.ChemicalToDiseaseRelationship_object, domain=ChemicalToDiseaseRelationship, range=Optional[Union[str, DiseaseId]]) - -slots.ChemicalToDiseaseRelationship_predicate = Slot(uri=DRUG.predicate, name="ChemicalToDiseaseRelationship_predicate", curie=DRUG.curie('predicate'), - model_uri=DRUG.ChemicalToDiseaseRelationship_predicate, domain=ChemicalToDiseaseRelationship, range=Optional[Union[str, ChemicalToDiseasePredicateId]]) - -slots.ChemicalToDiseaseRelationship_subject_qualifier = Slot(uri=DRUG.subject_qualifier, name="ChemicalToDiseaseRelationship_subject_qualifier", curie=DRUG.curie('subject_qualifier'), - model_uri=DRUG.ChemicalToDiseaseRelationship_subject_qualifier, domain=ChemicalToDiseaseRelationship, range=Optional[Union[str, NamedEntityId]]) - -slots.ChemicalToDiseaseRelationship_object_qualifier = Slot(uri=DRUG.object_qualifier, name="ChemicalToDiseaseRelationship_object_qualifier", curie=DRUG.curie('object_qualifier'), - model_uri=DRUG.ChemicalToDiseaseRelationship_object_qualifier, domain=ChemicalToDiseaseRelationship, range=Optional[Union[str, NamedEntityId]]) - -slots.Disease_id = Slot(uri=DRUG.id, name="Disease_id", curie=DRUG.curie('id'), - model_uri=DRUG.Disease_id, domain=Disease, range=Union[str, DiseaseId], - pattern=re.compile(r'^MESH:[CD][0-9]{6}$')) - -slots.Chemical_id = Slot(uri=DRUG.id, name="Chemical_id", curie=DRUG.curie('id'), - model_uri=DRUG.Chemical_id, domain=Chemical, range=Union[str, ChemicalId], - pattern=re.compile(r'^MESH:[CD][0-9]{6}$')) \ No newline at end of file diff --git a/projects/ctd/docs/AnnotatorResult.md b/projects/ctd/docs/AnnotatorResult.md deleted file mode 100644 index 1ea640ba8..000000000 --- a/projects/ctd/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [drug:AnnotatorResult](http://w3id.org/ontogpt/drug/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/ctd/docs/Any.md b/projects/ctd/docs/Any.md deleted file mode 100644 index 4da2d3785..000000000 --- a/projects/ctd/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [drug:Any](http://w3id.org/ontogpt/drug/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/ctd/docs/Chemical.md b/projects/ctd/docs/Chemical.md deleted file mode 100644 index 583be8e98..000000000 --- a/projects/ctd/docs/Chemical.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: Chemical - - - - -URI: [drug:Chemical](http://w3id.org/ontogpt/drug/Chemical) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[ChemicalToDiseaseRelationship],[ChemicalToDiseaseRelationship]-%20subject%200..1>[Chemical|id:string;label(i):string%20%3F],[NamedEntity]^-[Chemical])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[ChemicalToDiseaseRelationship],[ChemicalToDiseaseRelationship]-%20subject%200..1>[Chemical|id:string;label(i):string%20%3F],[NamedEntity]^-[Chemical]) - -## Identifier prefixes - - * MESH - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md)** *[ChemicalToDiseaseRelationship➞subject](ChemicalToDiseaseRelationship_subject.md)* <sub>0..1</sub> **[Chemical](Chemical.md)** - -## Attributes - - -### Own - - * [Chemical➞id](Chemical_id.md) <sub>1..1</sub> - * Range: [String](types/String.md) - -### Inherited from NamedEntity: - - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ctd/docs/ChemicalToDiseaseDocument.md b/projects/ctd/docs/ChemicalToDiseaseDocument.md deleted file mode 100644 index cfb2836e8..000000000 --- a/projects/ctd/docs/ChemicalToDiseaseDocument.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: ChemicalToDiseaseDocument - - -A document that contains chemical to disease relations. - -URI: [drug:ChemicalToDiseaseDocument](http://w3id.org/ontogpt/drug/ChemicalToDiseaseDocument) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples],[Publication],[ChemicalToDiseaseRelationship],[ChemicalToDiseaseRelationship]<triples%200..*-++[ChemicalToDiseaseDocument],[TextWithTriples]^-[ChemicalToDiseaseDocument])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples],[Publication],[ChemicalToDiseaseRelationship],[ChemicalToDiseaseRelationship]<triples%200..*-++[ChemicalToDiseaseDocument],[TextWithTriples]^-[ChemicalToDiseaseDocument]) - -## Parents - - * is_a: [TextWithTriples](TextWithTriples.md) - -## Referenced by Class - - -## Attributes - - -### Own - - * [ChemicalToDiseaseDocument➞triples](ChemicalToDiseaseDocument_triples.md) <sub>0..\*</sub> - * Range: [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) - -### Inherited from TextWithTriples: - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) diff --git a/projects/ctd/docs/ChemicalToDiseaseDocument_triples.md b/projects/ctd/docs/ChemicalToDiseaseDocument_triples.md deleted file mode 100644 index 3c08f751c..000000000 --- a/projects/ctd/docs/ChemicalToDiseaseDocument_triples.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: triples - - - - -URI: [drug:ChemicalToDiseaseDocument_triples](http://w3id.org/ontogpt/drug/ChemicalToDiseaseDocument_triples) - - -## Domain and Range - -[ChemicalToDiseaseDocument](ChemicalToDiseaseDocument.md) → <sub>0..\*</sub> [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) - -## Parents - - * is_a: [➞triples](textWithTriples__triples.md) - -## Children - - -## Used by - - * [ChemicalToDiseaseDocument](ChemicalToDiseaseDocument.md) diff --git a/projects/ctd/docs/ChemicalToDiseasePredicate.md b/projects/ctd/docs/ChemicalToDiseasePredicate.md deleted file mode 100644 index d41c9ffb4..000000000 --- a/projects/ctd/docs/ChemicalToDiseasePredicate.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Class: ChemicalToDiseasePredicate - - -A predicate for chemical to disease relationships - -URI: [drug:ChemicalToDiseasePredicate](http://w3id.org/ontogpt/drug/ChemicalToDiseasePredicate) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[ChemicalToDiseaseRelationship],[ChemicalToDiseaseRelationship]-%20predicate%200..1>[ChemicalToDiseasePredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ChemicalToDiseasePredicate])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[ChemicalToDiseaseRelationship],[ChemicalToDiseaseRelationship]-%20predicate%200..1>[ChemicalToDiseasePredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ChemicalToDiseasePredicate]) - -## Parents - - * is_a: [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md)** *[ChemicalToDiseaseRelationship➞predicate](ChemicalToDiseaseRelationship_predicate.md)* <sub>0..1</sub> **[ChemicalToDiseasePredicate](ChemicalToDiseasePredicate.md)** - -## Attributes - - -### Inherited from RelationshipType: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | for the purposes of evaluation against BC5CDR, any predicate other than INDUCES is ignored. | - diff --git a/projects/ctd/docs/ChemicalToDiseaseRelationship.md b/projects/ctd/docs/ChemicalToDiseaseRelationship.md deleted file mode 100644 index 5fa4aa7b2..000000000 --- a/projects/ctd/docs/ChemicalToDiseaseRelationship.md +++ /dev/null @@ -1,45 +0,0 @@ - -# Class: ChemicalToDiseaseRelationship - - -A triple where the subject is a chemical and the object is a disease. - -URI: [drug:ChemicalToDiseaseRelationship](http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[NamedEntity],[Disease],[NamedEntity]<object_qualifier%200..1-%20[ChemicalToDiseaseRelationship|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[ChemicalToDiseaseRelationship],[ChemicalToDiseasePredicate]<predicate%200..1-%20[ChemicalToDiseaseRelationship],[Disease]<object%200..1-%20[ChemicalToDiseaseRelationship],[Chemical]<subject%200..1-%20[ChemicalToDiseaseRelationship],[ChemicalToDiseaseDocument]++-%20triples%200..*>[ChemicalToDiseaseRelationship],[Triple]^-[ChemicalToDiseaseRelationship],[ChemicalToDiseasePredicate],[ChemicalToDiseaseDocument],[Chemical])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[NamedEntity],[Disease],[NamedEntity]<object_qualifier%200..1-%20[ChemicalToDiseaseRelationship|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[ChemicalToDiseaseRelationship],[ChemicalToDiseasePredicate]<predicate%200..1-%20[ChemicalToDiseaseRelationship],[Disease]<object%200..1-%20[ChemicalToDiseaseRelationship],[Chemical]<subject%200..1-%20[ChemicalToDiseaseRelationship],[ChemicalToDiseaseDocument]++-%20triples%200..*>[ChemicalToDiseaseRelationship],[Triple]^-[ChemicalToDiseaseRelationship],[ChemicalToDiseasePredicate],[ChemicalToDiseaseDocument],[Chemical]) - -## Parents - - * is_a: [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - * **[ChemicalToDiseaseDocument](ChemicalToDiseaseDocument.md)** *[ChemicalToDiseaseDocument➞triples](ChemicalToDiseaseDocument_triples.md)* <sub>0..\*</sub> **[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md)** - -## Attributes - - -### Own - - * [ChemicalToDiseaseRelationship➞subject](ChemicalToDiseaseRelationship_subject.md) <sub>0..1</sub> - * Description: The chemical substance, drug, or small molecule. For example: Lidocaine, Monosodium Glutamate, Imatinib. - * Range: [Chemical](Chemical.md) - * [ChemicalToDiseaseRelationship➞object](ChemicalToDiseaseRelationship_object.md) <sub>0..1</sub> - * Description: The disease or condition that is being treated or induced by the chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache. - * Range: [Disease](Disease.md) - * [ChemicalToDiseaseRelationship➞predicate](ChemicalToDiseaseRelationship_predicate.md) <sub>0..1</sub> - * Description: The relationship type, e.g. INDUCES, TREATS. - * Range: [ChemicalToDiseasePredicate](ChemicalToDiseasePredicate.md) - * [ChemicalToDiseaseRelationship➞subject_qualifier](ChemicalToDiseaseRelationship_subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the chemical, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [ChemicalToDiseaseRelationship➞object_qualifier](ChemicalToDiseaseRelationship_object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the disease, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) - -### Inherited from Triple: - - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) diff --git a/projects/ctd/docs/ChemicalToDiseaseRelationship_object.md b/projects/ctd/docs/ChemicalToDiseaseRelationship_object.md deleted file mode 100644 index 60be4e509..000000000 --- a/projects/ctd/docs/ChemicalToDiseaseRelationship_object.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object - - -The disease or condition that is being treated or induced by the chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache. - -URI: [drug:ChemicalToDiseaseRelationship_object](http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship_object) - - -## Domain and Range - -[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) → <sub>0..1</sub> [Disease](Disease.md) - -## Parents - - * is_a: [➞object](triple__object.md) - -## Children - - -## Used by - - * [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) diff --git a/projects/ctd/docs/ChemicalToDiseaseRelationship_object_qualifier.md b/projects/ctd/docs/ChemicalToDiseaseRelationship_object_qualifier.md deleted file mode 100644 index 41cbc9363..000000000 --- a/projects/ctd/docs/ChemicalToDiseaseRelationship_object_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the disease, e.g. "severe" or "with additional complications" - -URI: [drug:ChemicalToDiseaseRelationship_object_qualifier](http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship_object_qualifier) - - -## Domain and Range - -[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞object_qualifier](triple__object_qualifier.md) - -## Children - - -## Used by - - * [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) diff --git a/projects/ctd/docs/ChemicalToDiseaseRelationship_predicate.md b/projects/ctd/docs/ChemicalToDiseaseRelationship_predicate.md deleted file mode 100644 index 1bc5f372a..000000000 --- a/projects/ctd/docs/ChemicalToDiseaseRelationship_predicate.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: predicate - - -The relationship type, e.g. INDUCES, TREATS. - -URI: [drug:ChemicalToDiseaseRelationship_predicate](http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship_predicate) - - -## Domain and Range - -[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) → <sub>0..1</sub> [ChemicalToDiseasePredicate](ChemicalToDiseasePredicate.md) - -## Parents - - * is_a: [➞predicate](triple__predicate.md) - -## Children - - -## Used by - - * [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) diff --git a/projects/ctd/docs/ChemicalToDiseaseRelationship_subject.md b/projects/ctd/docs/ChemicalToDiseaseRelationship_subject.md deleted file mode 100644 index e4bee707d..000000000 --- a/projects/ctd/docs/ChemicalToDiseaseRelationship_subject.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject - - -The chemical substance, drug, or small molecule. For example: Lidocaine, Monosodium Glutamate, Imatinib. - -URI: [drug:ChemicalToDiseaseRelationship_subject](http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship_subject) - - -## Domain and Range - -[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) → <sub>0..1</sub> [Chemical](Chemical.md) - -## Parents - - * is_a: [➞subject](triple__subject.md) - -## Children - - -## Used by - - * [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) diff --git a/projects/ctd/docs/ChemicalToDiseaseRelationship_subject_qualifier.md b/projects/ctd/docs/ChemicalToDiseaseRelationship_subject_qualifier.md deleted file mode 100644 index 8a2ecee11..000000000 --- a/projects/ctd/docs/ChemicalToDiseaseRelationship_subject_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the chemical, e.g. "high dose" or "intravenously administered" - -URI: [drug:ChemicalToDiseaseRelationship_subject_qualifier](http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship_subject_qualifier) - - -## Domain and Range - -[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞subject_qualifier](triple__subject_qualifier.md) - -## Children - - -## Used by - - * [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) diff --git a/projects/ctd/docs/Chemical_id.md b/projects/ctd/docs/Chemical_id.md deleted file mode 100644 index 115bd91d8..000000000 --- a/projects/ctd/docs/Chemical_id.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: id - - - - -URI: [drug:Chemical_id](http://w3id.org/ontogpt/drug/Chemical_id) - - -## Domain and Range - -[Chemical](Chemical.md) → <sub>1..1</sub> [String](types/String.md) - -## Parents - - * is_a: [➞id](namedEntity__id.md) - -## Children - - -## Used by - - * [Chemical](Chemical.md) diff --git a/projects/ctd/docs/CompoundExpression.md b/projects/ctd/docs/CompoundExpression.md deleted file mode 100644 index 6c3865064..000000000 --- a/projects/ctd/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [drug:CompoundExpression](http://w3id.org/ontogpt/drug/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/ctd/docs/Disease.md b/projects/ctd/docs/Disease.md deleted file mode 100644 index f8468fbe8..000000000 --- a/projects/ctd/docs/Disease.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: Disease - - - - -URI: [drug:Disease](http://w3id.org/ontogpt/drug/Disease) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[ChemicalToDiseaseRelationship]-%20object%200..1>[Disease|id:string;label(i):string%20%3F],[NamedEntity]^-[Disease],[ChemicalToDiseaseRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[ChemicalToDiseaseRelationship]-%20object%200..1>[Disease|id:string;label(i):string%20%3F],[NamedEntity]^-[Disease],[ChemicalToDiseaseRelationship]) - -## Identifier prefixes - - * MESH - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md)** *[ChemicalToDiseaseRelationship➞object](ChemicalToDiseaseRelationship_object.md)* <sub>0..1</sub> **[Disease](Disease.md)** - -## Attributes - - -### Own - - * [Disease➞id](Disease_id.md) <sub>1..1</sub> - * Range: [String](types/String.md) - -### Inherited from NamedEntity: - - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ctd/docs/Disease_id.md b/projects/ctd/docs/Disease_id.md deleted file mode 100644 index 27b010dc2..000000000 --- a/projects/ctd/docs/Disease_id.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: id - - - - -URI: [drug:Disease_id](http://w3id.org/ontogpt/drug/Disease_id) - - -## Domain and Range - -[Disease](Disease.md) → <sub>1..1</sub> [String](types/String.md) - -## Parents - - * is_a: [➞id](namedEntity__id.md) - -## Children - - -## Used by - - * [Disease](Disease.md) diff --git a/projects/ctd/docs/ExtractionResult.md b/projects/ctd/docs/ExtractionResult.md deleted file mode 100644 index 7d07c8ae7..000000000 --- a/projects/ctd/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [drug:ExtractionResult](http://w3id.org/ontogpt/drug/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/ctd/docs/MeshChemicalIdentifier.md b/projects/ctd/docs/MeshChemicalIdentifier.md deleted file mode 100644 index 689558de6..000000000 --- a/projects/ctd/docs/MeshChemicalIdentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: MeshChemicalIdentifier - - - - -URI: [drug:MeshChemicalIdentifier](http://w3id.org/ontogpt/drug/MeshChemicalIdentifier) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/ctd/docs/MeshDiseaseIdentifier.md b/projects/ctd/docs/MeshDiseaseIdentifier.md deleted file mode 100644 index 7ae12796d..000000000 --- a/projects/ctd/docs/MeshDiseaseIdentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: MeshDiseaseIdentifier - - - - -URI: [drug:MeshDiseaseIdentifier](http://w3id.org/ontogpt/drug/MeshDiseaseIdentifier) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/ctd/docs/NamedEntity.md b/projects/ctd/docs/NamedEntity.md deleted file mode 100644 index b06a1df18..000000000 --- a/projects/ctd/docs/NamedEntity.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [drug:NamedEntity](http://w3id.org/ontogpt/drug/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[ChemicalToDiseaseRelationship]-%20object_qualifier%200..1>[NamedEntity|id:string;label:string%20%3F],[ChemicalToDiseaseRelationship]-%20subject_qualifier%200..1>[NamedEntity],[Triple]-%20object%200..1>[NamedEntity],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Disease],[NamedEntity]^-[Chemical],[Triple],[Disease],[ChemicalToDiseaseRelationship],[Chemical])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[ChemicalToDiseaseRelationship]-%20object_qualifier%200..1>[NamedEntity|id:string;label:string%20%3F],[ChemicalToDiseaseRelationship]-%20subject_qualifier%200..1>[NamedEntity],[Triple]-%20object%200..1>[NamedEntity],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Disease],[NamedEntity]^-[Chemical],[Triple],[Disease],[ChemicalToDiseaseRelationship],[Chemical]) - -## Children - - * [Chemical](Chemical.md) - * [Disease](Disease.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md)** *[ChemicalToDiseaseRelationship➞object_qualifier](ChemicalToDiseaseRelationship_object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **[ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md)** *[ChemicalToDiseaseRelationship➞subject_qualifier](ChemicalToDiseaseRelationship_subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ctd/docs/NullDataOptions.md b/projects/ctd/docs/NullDataOptions.md deleted file mode 100644 index 25c94dc0c..000000000 --- a/projects/ctd/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [drug:NullDataOptions](http://w3id.org/ontogpt/drug/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/ctd/docs/Publication.md b/projects/ctd/docs/Publication.md deleted file mode 100644 index 838ef88ac..000000000 --- a/projects/ctd/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [drug:Publication](http://w3id.org/ontogpt/drug/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/ctd/docs/RelationshipType.md b/projects/ctd/docs/RelationshipType.md deleted file mode 100644 index 937f4ba51..000000000 --- a/projects/ctd/docs/RelationshipType.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [drug:RelationshipType](http://w3id.org/ontogpt/drug/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ChemicalToDiseasePredicate],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity],[ChemicalToDiseasePredicate])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ChemicalToDiseasePredicate],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity],[ChemicalToDiseasePredicate]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Children - - * [ChemicalToDiseasePredicate](ChemicalToDiseasePredicate.md) - A predicate for chemical to disease relationships - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ctd/docs/TextWithTriples.md b/projects/ctd/docs/TextWithTriples.md deleted file mode 100644 index 3e244027c..000000000 --- a/projects/ctd/docs/TextWithTriples.md +++ /dev/null @@ -1,27 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [drug:TextWithTriples](http://w3id.org/ontogpt/drug/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[TextWithTriples]^-[ChemicalToDiseaseDocument],[Publication],[ChemicalToDiseaseDocument])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[TextWithTriples]^-[ChemicalToDiseaseDocument],[Publication],[ChemicalToDiseaseDocument]) - -## Children - - * [ChemicalToDiseaseDocument](ChemicalToDiseaseDocument.md) - A document that contains chemical to disease relations. - -## Referenced by Class - - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/ctd/docs/Triple.md b/projects/ctd/docs/Triple.md deleted file mode 100644 index 6768bc705..000000000 --- a/projects/ctd/docs/Triple.md +++ /dev/null @@ -1,43 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [drug:Triple](http://w3id.org/ontogpt/drug/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[Triple]^-[ChemicalToDiseaseRelationship],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression],[ChemicalToDiseaseRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[Triple]^-[ChemicalToDiseaseRelationship],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression],[ChemicalToDiseaseRelationship]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Children - - * [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) - A triple where the subject is a chemical and the object is a disease. - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/ctd/docs/annotatorResult__object_id.md b/projects/ctd/docs/annotatorResult__object_id.md deleted file mode 100644 index 3be702157..000000000 --- a/projects/ctd/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [drug:annotatorResult__object_id](http://w3id.org/ontogpt/drug/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ctd/docs/annotatorResult__object_text.md b/projects/ctd/docs/annotatorResult__object_text.md deleted file mode 100644 index 69b131f6a..000000000 --- a/projects/ctd/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [drug:annotatorResult__object_text](http://w3id.org/ontogpt/drug/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ctd/docs/annotatorResult__subject_text.md b/projects/ctd/docs/annotatorResult__subject_text.md deleted file mode 100644 index c72ea9131..000000000 --- a/projects/ctd/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [drug:annotatorResult__subject_text](http://w3id.org/ontogpt/drug/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ctd/docs/ctd.md b/projects/ctd/docs/ctd.md deleted file mode 100644 index 3388ac776..000000000 --- a/projects/ctd/docs/ctd.md +++ /dev/null @@ -1,119 +0,0 @@ - -# ctd - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for Chemical to Disease associations. -This template is intended to represent associations between chemicals and diseases, and for evaluating Semantic Llama against BioCreative V Chemical Disease Relation (CDR) Task (BC5CDR). - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) - A triple where the subject is a chemical and the object is a disease. - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [Chemical](Chemical.md) - * [Disease](Disease.md) - * [RelationshipType](RelationshipType.md) - * [ChemicalToDiseasePredicate](ChemicalToDiseasePredicate.md) - A predicate for chemical to disease relationships - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - * [ChemicalToDiseaseDocument](ChemicalToDiseaseDocument.md) - A document that contains chemical to disease relations. - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [Chemical➞id](Chemical_id.md) - * [Disease➞id](Disease_id.md) - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [ChemicalToDiseaseDocument➞triples](ChemicalToDiseaseDocument_triples.md) - * [➞object](triple__object.md) - * [ChemicalToDiseaseRelationship➞object](ChemicalToDiseaseRelationship_object.md) - The disease or condition that is being treated or induced by the chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache. - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [ChemicalToDiseaseRelationship➞object_qualifier](ChemicalToDiseaseRelationship_object_qualifier.md) - An optional qualifier or modifier for the disease, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [ChemicalToDiseaseRelationship➞predicate](ChemicalToDiseaseRelationship_predicate.md) - The relationship type, e.g. INDUCES, TREATS. - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [ChemicalToDiseaseRelationship➞subject](ChemicalToDiseaseRelationship_subject.md) - The chemical substance, drug, or small molecule. For example: Lidocaine, Monosodium Glutamate, Imatinib. - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * [ChemicalToDiseaseRelationship➞subject_qualifier](ChemicalToDiseaseRelationship_subject_qualifier.md) - An optional qualifier or modifier for the chemical, e.g. "high dose" or "intravenously administered" - -### Enums - - * [MeshChemicalIdentifier](MeshChemicalIdentifier.md) - * [MeshDiseaseIdentifier](MeshDiseaseIdentifier.md) - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/ctd/docs/extractionResult__extracted_object.md b/projects/ctd/docs/extractionResult__extracted_object.md deleted file mode 100644 index 9e1ffec86..000000000 --- a/projects/ctd/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [drug:extractionResult__extracted_object](http://w3id.org/ontogpt/drug/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ctd/docs/extractionResult__input_id.md b/projects/ctd/docs/extractionResult__input_id.md deleted file mode 100644 index 3091924ef..000000000 --- a/projects/ctd/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [drug:extractionResult__input_id](http://w3id.org/ontogpt/drug/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ctd/docs/extractionResult__input_text.md b/projects/ctd/docs/extractionResult__input_text.md deleted file mode 100644 index e52590f86..000000000 --- a/projects/ctd/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [drug:extractionResult__input_text](http://w3id.org/ontogpt/drug/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ctd/docs/extractionResult__input_title.md b/projects/ctd/docs/extractionResult__input_title.md deleted file mode 100644 index db5911166..000000000 --- a/projects/ctd/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [drug:extractionResult__input_title](http://w3id.org/ontogpt/drug/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ctd/docs/extractionResult__named_entities.md b/projects/ctd/docs/extractionResult__named_entities.md deleted file mode 100644 index 5d7701c98..000000000 --- a/projects/ctd/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [drug:extractionResult__named_entities](http://w3id.org/ontogpt/drug/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ctd/docs/extractionResult__prompt.md b/projects/ctd/docs/extractionResult__prompt.md deleted file mode 100644 index dc94587a9..000000000 --- a/projects/ctd/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [drug:extractionResult__prompt](http://w3id.org/ontogpt/drug/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ctd/docs/extractionResult__raw_completion_output.md b/projects/ctd/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 1e77ca0a5..000000000 --- a/projects/ctd/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [drug:extractionResult__raw_completion_output](http://w3id.org/ontogpt/drug/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ctd/docs/namedEntity__id.md b/projects/ctd/docs/namedEntity__id.md deleted file mode 100644 index d5667e862..000000000 --- a/projects/ctd/docs/namedEntity__id.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [drug:namedEntity__id](http://w3id.org/ontogpt/drug/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - * [Chemical➞id](Chemical_id.md) - * [Disease➞id](Disease_id.md) - -## Used by - - * [ChemicalToDiseasePredicate](ChemicalToDiseasePredicate.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/ctd/docs/namedEntity__label.md b/projects/ctd/docs/namedEntity__label.md deleted file mode 100644 index 23898591a..000000000 --- a/projects/ctd/docs/namedEntity__label.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [drug:namedEntity__label](http://w3id.org/ontogpt/drug/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Chemical](Chemical.md) - * [ChemicalToDiseasePredicate](ChemicalToDiseasePredicate.md) - * [Disease](Disease.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/ctd/docs/publication__abstract.md b/projects/ctd/docs/publication__abstract.md deleted file mode 100644 index f72aeea74..000000000 --- a/projects/ctd/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [drug:publication__abstract](http://w3id.org/ontogpt/drug/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ctd/docs/publication__combined_text.md b/projects/ctd/docs/publication__combined_text.md deleted file mode 100644 index 5e743fb57..000000000 --- a/projects/ctd/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [drug:publication__combined_text](http://w3id.org/ontogpt/drug/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ctd/docs/publication__full_text.md b/projects/ctd/docs/publication__full_text.md deleted file mode 100644 index 7612a1e21..000000000 --- a/projects/ctd/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [drug:publication__full_text](http://w3id.org/ontogpt/drug/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ctd/docs/publication__id.md b/projects/ctd/docs/publication__id.md deleted file mode 100644 index 6559e9615..000000000 --- a/projects/ctd/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [drug:publication__id](http://w3id.org/ontogpt/drug/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ctd/docs/publication__title.md b/projects/ctd/docs/publication__title.md deleted file mode 100644 index 5f67aee85..000000000 --- a/projects/ctd/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [drug:publication__title](http://w3id.org/ontogpt/drug/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ctd/docs/textWithTriples__publication.md b/projects/ctd/docs/textWithTriples__publication.md deleted file mode 100644 index d6b4fa34d..000000000 --- a/projects/ctd/docs/textWithTriples__publication.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: publication - - - - -URI: [drug:textWithTriples__publication](http://w3id.org/ontogpt/drug/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [ChemicalToDiseaseDocument](ChemicalToDiseaseDocument.md) - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ctd/docs/textWithTriples__triples.md b/projects/ctd/docs/textWithTriples__triples.md deleted file mode 100644 index c7cf5bb44..000000000 --- a/projects/ctd/docs/textWithTriples__triples.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: triples - - - - -URI: [drug:textWithTriples__triples](http://w3id.org/ontogpt/drug/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - * [ChemicalToDiseaseDocument➞triples](ChemicalToDiseaseDocument_triples.md) - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ctd/docs/triple__object.md b/projects/ctd/docs/triple__object.md deleted file mode 100644 index a2b3698de..000000000 --- a/projects/ctd/docs/triple__object.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object - - - - -URI: [drug:triple__object](http://w3id.org/ontogpt/drug/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [ChemicalToDiseaseRelationship➞object](ChemicalToDiseaseRelationship_object.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ctd/docs/triple__object_qualifier.md b/projects/ctd/docs/triple__object_qualifier.md deleted file mode 100644 index dc1efb4ab..000000000 --- a/projects/ctd/docs/triple__object_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [drug:triple__object_qualifier](http://w3id.org/ontogpt/drug/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [ChemicalToDiseaseRelationship➞object_qualifier](ChemicalToDiseaseRelationship_object_qualifier.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ctd/docs/triple__predicate.md b/projects/ctd/docs/triple__predicate.md deleted file mode 100644 index a9b9ac83a..000000000 --- a/projects/ctd/docs/triple__predicate.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: predicate - - - - -URI: [drug:triple__predicate](http://w3id.org/ontogpt/drug/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - * [ChemicalToDiseaseRelationship➞predicate](ChemicalToDiseaseRelationship_predicate.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ctd/docs/triple__qualifier.md b/projects/ctd/docs/triple__qualifier.md deleted file mode 100644 index 9ecf6f540..000000000 --- a/projects/ctd/docs/triple__qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [drug:triple__qualifier](http://w3id.org/ontogpt/drug/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ChemicalToDiseaseRelationship](ChemicalToDiseaseRelationship.md) - * [Triple](Triple.md) diff --git a/projects/ctd/docs/triple__subject.md b/projects/ctd/docs/triple__subject.md deleted file mode 100644 index 9378144c0..000000000 --- a/projects/ctd/docs/triple__subject.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject - - - - -URI: [drug:triple__subject](http://w3id.org/ontogpt/drug/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [ChemicalToDiseaseRelationship➞subject](ChemicalToDiseaseRelationship_subject.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ctd/docs/triple__subject_qualifier.md b/projects/ctd/docs/triple__subject_qualifier.md deleted file mode 100644 index 05061102a..000000000 --- a/projects/ctd/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [drug:triple__subject_qualifier](http://w3id.org/ontogpt/drug/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [ChemicalToDiseaseRelationship➞subject_qualifier](ChemicalToDiseaseRelationship_subject_qualifier.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ctd/docs/types/Boolean.md b/projects/ctd/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/ctd/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/ctd/docs/types/Curie.md b/projects/ctd/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/ctd/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/ctd/docs/types/Date.md b/projects/ctd/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/ctd/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/ctd/docs/types/DateOrDatetime.md b/projects/ctd/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/ctd/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ctd/docs/types/Datetime.md b/projects/ctd/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/ctd/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/ctd/docs/types/Decimal.md b/projects/ctd/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/ctd/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/ctd/docs/types/Double.md b/projects/ctd/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/ctd/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/ctd/docs/types/Float.md b/projects/ctd/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/ctd/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/ctd/docs/types/Integer.md b/projects/ctd/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/ctd/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/ctd/docs/types/Jsonpath.md b/projects/ctd/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/ctd/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ctd/docs/types/Jsonpointer.md b/projects/ctd/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/ctd/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ctd/docs/types/Ncname.md b/projects/ctd/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/ctd/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/ctd/docs/types/Nodeidentifier.md b/projects/ctd/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/ctd/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/ctd/docs/types/Objectidentifier.md b/projects/ctd/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/ctd/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/ctd/docs/types/Sparqlpath.md b/projects/ctd/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/ctd/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ctd/docs/types/String.md b/projects/ctd/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/ctd/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/ctd/docs/types/Time.md b/projects/ctd/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/ctd/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/ctd/docs/types/Uri.md b/projects/ctd/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/ctd/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/ctd/docs/types/Uriorcurie.md b/projects/ctd/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/ctd/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/ctd/excel/ctd.xlsx b/projects/ctd/excel/ctd.xlsx deleted file mode 100644 index 68d93db871c737d13dffa7f0947fe071b12fb01f..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 9684 zcmeHtbyU<}w>RD0(nv~oOEZ)VAl>bNbVwuJJ(SXov<M8P(xG%nHz*(=DIM>i>pnhm z^<BTU-uJHi&ogU%XPC8Se>mr}&pw~M_c^Lc@CXDjFfb@EF<Qvl0KGPhK<Kw>=z{}& zEF8>LogExqI7}TK**)xRm1C9B+c|M$ZWK4??KStPxv0nUmp*vQ3-HHVNV|nx`lz?X z&5AB?MmG_D)aj&k=L_vDevbP=4hDh_=#U;OxhF?YYOO;lG3XhEKMm@ndrj5@Z$kKp 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z#`2>qzl(CWs{A#hJi<SsaQ&z;@50<IfPTS<5&s$HM>%vC=5F@>FBsTfXyX$)r(e1J zUDLbC*Dq5Uvfom%yM}j@nO}x%<o_D_f2B5ejqgg~FJo59AI5(X#=AIo<>D8PD%Bsw YLsbb8dcWsZTkv5n5ny22sc*miA5b%LQUCw| diff --git a/projects/ctd/graphql/ctd.graphql b/projects/ctd/graphql/ctd.graphql deleted file mode 100644 index 0c020b012..000000000 --- a/projects/ctd/graphql/ctd.graphql +++ /dev/null @@ -1,97 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type Chemical - { - label: String - id: String! - } - -type ChemicalToDiseaseDocument - { - publication: Publication - triples: [ChemicalToDiseaseRelationship] - } - -type ChemicalToDiseasePredicate - { - id: String! - label: String - } - -type ChemicalToDiseaseRelationship - { - qualifier: String - subject: Chemical - object: Disease - predicate: ChemicalToDiseasePredicate - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - -interface CompoundExpression - { - } - -type Disease - { - label: String - id: String! - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/ctd/jsonld/ctd.context.jsonld b/projects/ctd/jsonld/ctd.context.jsonld deleted file mode 100644 index b400329ed..000000000 --- a/projects/ctd/jsonld/ctd.context.jsonld +++ /dev/null @@ -1,128 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:52:15", - "source": "ctd.yaml" - }, - "@context": { - "MESH": "http://example.org/UNKNOWN/MESH/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "drug": "http://w3id.org/ontogpt/drug/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/drug/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "id": { - "@id": "core:id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/ctd/jsonld/ctd.jsonld b/projects/ctd/jsonld/ctd.jsonld deleted file mode 100644 index e92a5d975..000000000 --- a/projects/ctd/jsonld/ctd.jsonld +++ /dev/null @@ -1,1303 +0,0 @@ -{ - "name": "ctd", - "description": "A template for Chemical to Disease associations.\nThis template is intended to represent associations between chemicals and diseases, and for evaluating Semantic Llama against BioCreative V Chemical Disease Relation (CDR) Task (BC5CDR).", - "title": "Chemical to Disease Template", - "source": "https://biocreative.bioinformatics.udel.edu/tasks/biocreative-v/track-3-cdr/", - "see_also": [ - "https://biocreative.bioinformatics.udel.edu/media/store/files/2015/BC5CDR_overview.final.pdf", - "https://academic.oup.com/database/article/doi/10.1093/database/baw068/2630414" - ], - "id": "http://w3id.org/ontogpt/ctd", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "drug", - "prefix_reference": "http://w3id.org/ontogpt/drug/" - } - ], - "default_prefix": "drug", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "MeshChemicalIdentifier", - "definition_uri": "http://w3id.org/ontogpt/drug/MeshChemicalIdentifier", - "from_schema": "http://w3id.org/ontogpt/ctd", - "reachable_from": { - "source_ontology": "obo:mesh", - "source_nodes": [ - "MESH:D000602", - "MESH:D001685", - "MESH:D002241", - "MESH:D004364", - "MESH:D006571", - "MESH:D007287", - "MESH:D008055", - "MESH:D009706", - "MESH:D009930", - "MESH:D011083", - "MESH:D013812", - "MESH:D019602", - "MESH:D045424", - "MESH:D045762", - "MESH:D046911" - ] - } - }, - { - "name": "MeshDiseaseIdentifier", - "definition_uri": "http://w3id.org/ontogpt/drug/MeshDiseaseIdentifier", - "from_schema": "http://w3id.org/ontogpt/ctd", - "reachable_from": { - "source_ontology": "obo:mesh", - "source_nodes": [ - "MESH:D001423", - "MESH:D001523", - "MESH:D002318", - "MESH:D002943", - "MESH:D004066", - "MESH:D004700", - "MESH:D005128", - "MESH:D005261", - "MESH:D006425", - "MESH:D007154", - "MESH:D007280", - "MESH:D009057", - "MESH:D009140", - "MESH:D009358", - "MESH:D009369", - "MESH:D009422", - "MESH:D009750", - "MESH:D009784", - "MESH:D010038", - "MESH:D010272", - "MESH:D012140", - "MESH:D013568", - "MESH:D014777", - "MESH:D014947", - "MESH:D017437", - "MESH:D052801", - "MESH:D064419" - ] - } - }, - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ChemicalToDiseaseDocument_triples", - "annotations": [ - { - "tag": "prompt", - "value": "A semi-colon separated list of chemical to disease relationships, where the relationship is either INDUCES or TREATS. for example: Lidocaine INDUCES cardiac asystole; Hydroxychloroquine NOT TREATS COVID-19; Methyldopa INDUCES Hypotension; Monosodium Glutamate NOT INDUCES Headache; Imatinib TREATS cancer", - "@type": "Annotation" - }, - { - "tag": "exclude", - "value": "Lidocaine, cardiac asystole, Hydroxychloroquine, COVID-19, Methyldopa, Headache, Imatinib, cancer", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "textWithTriples__triples", - "domain": "ChemicalToDiseaseDocument", - "slot_uri": "http://w3id.org/ontogpt/drug/triples", - "multivalued": true, - "alias": "triples", - "owner": "ChemicalToDiseaseDocument", - "domain_of": [ - "ChemicalToDiseaseDocument" - ], - "is_usage_slot": true, - "usage_slot_name": "triples", - "range": "ChemicalToDiseaseRelationship", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "ChemicalToDiseaseRelationship_subject", - "description": "The chemical substance, drug, or small molecule. For example: Lidocaine, Monosodium Glutamate, Imatinib.", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "triple__subject", - "domain": "ChemicalToDiseaseRelationship", - "slot_uri": "http://w3id.org/ontogpt/drug/subject", - "alias": "subject", - "owner": "ChemicalToDiseaseRelationship", - "domain_of": [ - "ChemicalToDiseaseRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "subject", - "range": "Chemical", - "@type": "SlotDefinition" - }, - { - "name": "ChemicalToDiseaseRelationship_object", - "description": "The disease or condition that is being treated or induced by the chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache.", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "triple__object", - "domain": "ChemicalToDiseaseRelationship", - "slot_uri": "http://w3id.org/ontogpt/drug/object", - "alias": "object", - "owner": "ChemicalToDiseaseRelationship", - "domain_of": [ - "ChemicalToDiseaseRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "object", - "range": "Disease", - "@type": "SlotDefinition" - }, - { - "name": "ChemicalToDiseaseRelationship_predicate", - "description": "The relationship type, e.g. INDUCES, TREATS.", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "triple__predicate", - "domain": "ChemicalToDiseaseRelationship", - "slot_uri": "http://w3id.org/ontogpt/drug/predicate", - "alias": "predicate", - "owner": "ChemicalToDiseaseRelationship", - "domain_of": [ - "ChemicalToDiseaseRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "predicate", - "range": "ChemicalToDiseasePredicate", - "@type": "SlotDefinition" - }, - { - "name": "ChemicalToDiseaseRelationship_subject_qualifier", - "description": "An optional qualifier or modifier for the chemical, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "triple__subject_qualifier", - "domain": "ChemicalToDiseaseRelationship", - "slot_uri": "http://w3id.org/ontogpt/drug/subject_qualifier", - "alias": "subject_qualifier", - "owner": "ChemicalToDiseaseRelationship", - "domain_of": [ - "ChemicalToDiseaseRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "subject_qualifier", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "ChemicalToDiseaseRelationship_object_qualifier", - "description": "An optional qualifier or modifier for the disease, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "triple__object_qualifier", - "domain": "ChemicalToDiseaseRelationship", - "slot_uri": "http://w3id.org/ontogpt/drug/object_qualifier", - "alias": "object_qualifier", - "owner": "ChemicalToDiseaseRelationship", - "domain_of": [ - "ChemicalToDiseaseRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "object_qualifier", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "Disease_id", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "namedEntity__id", - "values_from": [ - "MeshDiseaseIdentifier" - ], - "domain": "Disease", - "slot_uri": "http://w3id.org/ontogpt/drug/id", - "identifier": true, - "alias": "id", - "owner": "Disease", - "domain_of": [ - "Disease" - ], - "is_usage_slot": true, - "usage_slot_name": "id", - "range": "string", - "required": true, - "pattern": "^MESH:[CD][0-9]{6}$", - "@type": "SlotDefinition" - }, - { - "name": "Chemical_id", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "namedEntity__id", - "values_from": [ - "MeshChemicalIdentifier" - ], - "domain": "Chemical", - "slot_uri": "http://w3id.org/ontogpt/drug/id", - "identifier": true, - "alias": "id", - "owner": "Chemical", - "domain_of": [ - "Chemical" - ], - "is_usage_slot": true, - "usage_slot_name": "id", - "range": "string", - "required": true, - "pattern": "^MESH:[CD][0-9]{6}$", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "ChemicalToDiseaseDocument", - "definition_uri": "http://w3id.org/ontogpt/drug/ChemicalToDiseaseDocument", - "description": "A document that contains chemical to disease relations.", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "TextWithTriples", - "slots": [ - "textWithTriples__publication", - "ChemicalToDiseaseDocument_triples" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/ChemicalToDiseaseDocument", - "@type": "ClassDefinition" - }, - { - "name": "ChemicalToDiseaseRelationship", - "definition_uri": "http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship", - "description": "A triple where the subject is a chemical and the object is a disease.", - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "Triple", - "slots": [ - "triple__qualifier", - "ChemicalToDiseaseRelationship_subject", - "ChemicalToDiseaseRelationship_object", - "ChemicalToDiseaseRelationship_predicate", - "ChemicalToDiseaseRelationship_subject_qualifier", - "ChemicalToDiseaseRelationship_object_qualifier" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship", - "@type": "ClassDefinition" - }, - { - "name": "Disease", - "id_prefixes": [ - "MESH" - ], - "definition_uri": "http://w3id.org/ontogpt/drug/Disease", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid, bioportal:meddra", - "@type": "Annotation" - }, - { - "tag": "prompt.examples", - "value": "cardiac asystole, COVID-19, Headache, cancer", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__label", - "Disease_id" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/Disease", - "@type": "ClassDefinition" - }, - { - "name": "Chemical", - "id_prefixes": [ - "MESH" - ], - "definition_uri": "http://w3id.org/ontogpt/drug/Chemical", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank, gilda:", - "@type": "Annotation" - }, - { - "tag": "prompt.examples", - "value": "Lidocaine, Hydroxychloroquine, Methyldopa, Imatinib", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__label", - "Chemical_id" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/Chemical", - "@type": "ClassDefinition" - }, - { - "name": "ChemicalToDiseasePredicate", - "definition_uri": "http://w3id.org/ontogpt/drug/ChemicalToDiseasePredicate", - "description": "A predicate for chemical to disease relationships", - "comments": [ - "for the purposes of evaluation against BC5CDR, any predicate other than INDUCES is ignored." - ], - "from_schema": "http://w3id.org/ontogpt/ctd", - "is_a": "RelationshipType", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/ChemicalToDiseasePredicate", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "ctd.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 6683, - "generation_date": "2023-08-07T10:52:16", - "@type": "SchemaDefinition", - "@context": [ - "projects/ctd/jsonld/ctd.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/drug/" - } - ] -} diff --git a/projects/ctd/jsonschema/ctd.schema.json b/projects/ctd/jsonschema/ctd.schema.json deleted file mode 100644 index 81c32600a..000000000 --- a/projects/ctd/jsonschema/ctd.schema.json +++ /dev/null @@ -1,261 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "Chemical": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "pattern": "^MESH:[CD][0-9]{6}$", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Chemical", - "type": "object" - }, - "ChemicalToDiseaseDocument": { - "additionalProperties": false, - "description": "A document that contains chemical to disease relations.", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/ChemicalToDiseaseRelationship" - }, - "type": "array" - } - }, - "title": "ChemicalToDiseaseDocument", - "type": "object" - }, - "ChemicalToDiseasePredicate": { - "additionalProperties": false, - "description": "A predicate for chemical to disease relationships", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ChemicalToDiseasePredicate", - "type": "object" - }, - "ChemicalToDiseaseRelationship": { - "additionalProperties": false, - "description": "A triple where the subject is a chemical and the object is a disease.", - "properties": { - "object": { - "description": "The disease or condition that is being treated or induced by the chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache.", - "type": "string" - }, - "object_qualifier": { - "description": "An optional qualifier or modifier for the disease, e.g. \"severe\" or \"with additional complications\"", - "type": "string" - }, - "predicate": { - "description": "The relationship type, e.g. INDUCES, TREATS.", - "type": "string" - }, - "qualifier": { - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "type": "string" - }, - "subject": { - "description": "The chemical substance, drug, or small molecule. For example: Lidocaine, Monosodium Glutamate, Imatinib.", - "type": "string" - }, - "subject_qualifier": { - "description": "An optional qualifier or modifier for the chemical, e.g. \"high dose\" or \"intravenously administered\"", - "type": "string" - } - }, - "title": "ChemicalToDiseaseRelationship", - "type": "object" - }, - "Disease": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "pattern": "^MESH:[CD][0-9]{6}$", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Disease", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "MeshChemicalIdentifier": { - "description": "", - "enum": [], - "title": "MeshChemicalIdentifier", - "type": "string" - }, - "MeshDiseaseIdentifier": { - "description": "", - "enum": [], - "title": "MeshDiseaseIdentifier", - "type": "string" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/ctd", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "ctd", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/ctd/owl/ctd.owl.ttl b/projects/ctd/owl/ctd.owl.ttl deleted file mode 100644 index 699f47674..000000000 --- a/projects/ctd/owl/ctd.owl.ttl +++ /dev/null @@ -1,500 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix drug: <http://w3id.org/ontogpt/drug/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/ctd> a owl:Ontology ; - rdfs:label "ctd" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples> ; - linkml:classes "{'ChemicalToDiseaseDocument': ClassDefinition(name='ChemicalToDiseaseDocument', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/ChemicalToDiseaseDocument', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A document that contains chemical to disease relations.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ctd', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='TextWithTriples', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'ChemicalToDiseaseDocument_triples'], slot_usage={'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='A semi-colon separated list of chemical to disease relationships, where the relationship is either INDUCES or TREATS. for example: Lidocaine INDUCES cardiac asystole; Hydroxychloroquine NOT TREATS COVID-19; Methyldopa INDUCES Hypotension; Monosodium Glutamate NOT INDUCES Headache; Imatinib TREATS cancer', extensions={}, annotations={}), 'exclude': Annotation(tag='exclude', value='Lidocaine, cardiac asystole, Hydroxychloroquine, COVID-19, Methyldopa, Headache, Imatinib, cancer', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='textWithTriples__triples', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalToDiseaseRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='drug:ChemicalToDiseaseDocument', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ChemicalToDiseaseRelationship': ClassDefinition(name='ChemicalToDiseaseRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/ChemicalToDiseaseRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A triple where the subject is a chemical and the object is a disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ctd', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='Triple', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__qualifier', 'ChemicalToDiseaseRelationship_subject', 'ChemicalToDiseaseRelationship_object', 'ChemicalToDiseaseRelationship_predicate', 'ChemicalToDiseaseRelationship_subject_qualifier', 'ChemicalToDiseaseRelationship_object_qualifier'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The chemical substance, drug, or small molecule. For example: Lidocaine, Monosodium Glutamate, Imatinib.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Chemical', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The disease or condition that is being treated or induced by the chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The relationship type, e.g. INDUCES, TREATS.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__predicate', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalToDiseasePredicate', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the chemical, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the disease, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='drug:ChemicalToDiseaseRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Disease': ClassDefinition(name='Disease', id_prefixes=['MESH'], definition_uri='http://w3id.org/ontogpt/drug/Disease', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid, bioportal:meddra', extensions={}, annotations={}), 'prompt.examples': Annotation(tag='prompt.examples', value='cardiac asystole, COVID-19, Headache, cancer', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ctd', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__label', 'Disease_id'], slot_usage={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='namedEntity__id', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['MeshDiseaseIdentifier'], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern='^MESH:[CD][0-9]{6}$', structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='drug:Disease', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Chemical': ClassDefinition(name='Chemical', id_prefixes=['MESH'], definition_uri='http://w3id.org/ontogpt/drug/Chemical', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank, gilda:', extensions={}, annotations={}), 'prompt.examples': Annotation(tag='prompt.examples', value='Lidocaine, Hydroxychloroquine, Methyldopa, Imatinib', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ctd', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__label', 'Chemical_id'], slot_usage={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='namedEntity__id', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['MeshChemicalIdentifier'], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern='^MESH:[CD][0-9]{6}$', structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='drug:Chemical', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ChemicalToDiseasePredicate': ClassDefinition(name='ChemicalToDiseasePredicate', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/ChemicalToDiseasePredicate', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A predicate for chemical to disease relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['for the purposes of evaluation against BC5CDR, any predicate other than INDUCES is ignored.'], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ctd', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='RelationshipType', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='drug:ChemicalToDiseasePredicate', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'MeshChemicalIdentifier': EnumDefinition(name='MeshChemicalIdentifier', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/MeshChemicalIdentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ctd', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:mesh', source_nodes=['MESH:D000602', 'MESH:D001685', 'MESH:D002241', 'MESH:D004364', 'MESH:D006571', 'MESH:D007287', 'MESH:D008055', 'MESH:D009706', 'MESH:D009930', 'MESH:D011083', 'MESH:D013812', 'MESH:D019602', 'MESH:D045424', 'MESH:D045762', 'MESH:D046911'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'MeshDiseaseIdentifier': EnumDefinition(name='MeshDiseaseIdentifier', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/MeshDiseaseIdentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ctd', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:mesh', source_nodes=['MESH:D001423', 'MESH:D001523', 'MESH:D002318', 'MESH:D002943', 'MESH:D004066', 'MESH:D004700', 'MESH:D005128', 'MESH:D005261', 'MESH:D006425', 'MESH:D007154', 'MESH:D007280', 'MESH:D009057', 'MESH:D009140', 'MESH:D009358', 'MESH:D009369', 'MESH:D009422', 'MESH:D009750', 'MESH:D009784', 'MESH:D010038', 'MESH:D010272', 'MESH:D012140', 'MESH:D013568', 'MESH:D014777', 'MESH:D014947', 'MESH:D017437', 'MESH:D052801', 'MESH:D064419'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/ctd" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -drug:MeshChemicalIdentifier a owl:Class, - linkml:EnumDefinition ; - rdfs:label "MeshChemicalIdentifier" ; - owl:unionOf [ rdf:rest () ] . - -drug:MeshDiseaseIdentifier a owl:Class, - linkml:EnumDefinition ; - rdfs:label "MeshDiseaseIdentifier" ; - owl:unionOf [ rdf:rest () ] . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - drug:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -drug:ChemicalToDiseaseDocument a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalToDiseaseDocument" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom drug:ChemicalToDiseaseRelationship ; - owl:onProperty drug:triples ], - <http://w3id.org/ontogpt/core/TextWithTriples> ; - skos:definition "A document that contains chemical to disease relations." ; - linkml:attributes "{}" ; - linkml:is_a "TextWithTriples" . - -drug:object a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:domain drug:ChemicalToDiseaseRelationship ; - rdfs:range drug:Disease ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/object> ; - skos:definition "The disease or condition that is being treated or induced by the chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache." ; - linkml:is_a "triple__object" . - -drug:object_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:domain drug:ChemicalToDiseaseRelationship ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/object_qualifier> ; - skos:definition "An optional qualifier or modifier for the disease, e.g. \"severe\" or \"with additional complications\"" ; - linkml:is_a "triple__object_qualifier" . - -drug:predicate a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:domain drug:ChemicalToDiseaseRelationship ; - rdfs:range drug:ChemicalToDiseasePredicate ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/predicate> ; - skos:definition "The relationship type, e.g. INDUCES, TREATS." ; - linkml:is_a "triple__predicate" . - -drug:subject a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:domain drug:ChemicalToDiseaseRelationship ; - rdfs:range drug:Chemical ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/subject> ; - skos:definition "The chemical substance, drug, or small molecule. For example: Lidocaine, Monosodium Glutamate, Imatinib." ; - linkml:is_a "triple__subject" . - -drug:subject_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:domain drug:ChemicalToDiseaseRelationship ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/subject_qualifier> ; - skos:definition "An optional qualifier or modifier for the chemical, e.g. \"high dose\" or \"intravenously administered\"" ; - linkml:is_a "triple__subject_qualifier" . - -drug:triples a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - drug:exclude "Lidocaine, cardiac asystole, Hydroxychloroquine, COVID-19, Methyldopa, Headache, Imatinib, cancer" ; - drug:prompt "A semi-colon separated list of chemical to disease relationships, where the relationship is either INDUCES or TREATS. for example: Lidocaine INDUCES cardiac asystole; Hydroxychloroquine NOT TREATS COVID-19; Methyldopa INDUCES Hypotension; Monosodium Glutamate NOT INDUCES Headache; Imatinib TREATS cancer" ; - rdfs:domain drug:ChemicalToDiseaseDocument ; - rdfs:range drug:ChemicalToDiseaseRelationship ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/triples> ; - linkml:is_a "textWithTriples__triples" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - drug:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -drug:ChemicalToDiseasePredicate a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalToDiseasePredicate" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/RelationshipType> ; - skos:definition "A predicate for chemical to disease relationships" ; - linkml:attributes "{}" ; - linkml:is_a "RelationshipType" . - -drug:id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "id" ; - rdfs:domain drug:Chemical, - drug:Disease ; - rdfs:range linkml:String ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/id> ; - linkml:is_a "namedEntity__id" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -drug:Chemical a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Chemical" ; - drug:annotators "sqlite:obo:mesh, sqlite:obo:chebi, sqlite:obo:ncit, bioportal:mdm, sqlite:obo:drugbank, gilda:" ; - drug:prompt.examples "Lidocaine, Hydroxychloroquine, Methyldopa, Imatinib" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty drug:id ; - owl:qualifiedCardinality 1 ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -drug:Disease a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Disease" ; - drug:annotators "sqlite:obo:mesh, sqlite:obo:mondo, sqlite:obo:hp, sqlite:obo:ncit, sqlite:obo:doid, bioportal:meddra" ; - drug:prompt.examples "cardiac asystole, COVID-19, Headache, cancer" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty drug:id ; - owl:qualifiedCardinality 1 ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -drug:ChemicalToDiseaseRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalToDiseaseRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass drug:Chemical ; - owl:onProperty drug:subject ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass drug:ChemicalToDiseasePredicate ; - owl:onProperty drug:predicate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty drug:subject_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty drug:object_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass drug:Disease ; - owl:onProperty drug:object ], - <http://w3id.org/ontogpt/core/Triple> ; - skos:definition "A triple where the subject is a chemical and the object is a disease." ; - linkml:attributes "{}" ; - linkml:is_a "Triple" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/ctd/prefixmap/ctd.yaml b/projects/ctd/prefixmap/ctd.yaml deleted file mode 100644 index 4100280b3..000000000 --- a/projects/ctd/prefixmap/ctd.yaml +++ /dev/null @@ -1,36 +0,0 @@ -{ - "MESH": "http://example.org/UNKNOWN/MESH/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "drug": "http://w3id.org/ontogpt/drug/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/ctd/protobuf/ctd.proto b/projects/ctd/protobuf/ctd.proto deleted file mode 100644 index 5fd0e70fe..000000000 --- a/projects/ctd/protobuf/ctd.proto +++ /dev/null @@ -1,67 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message Chemical - { - string label = 0 - string id = 0 - } -// A document that contains chemical to disease relations. -message ChemicalToDiseaseDocument - { - publication publication = 0 - repeated chemicalToDiseaseRelationship triples = 0 - } -// A predicate for chemical to disease relationships -message ChemicalToDiseasePredicate - { - string id = 0 - string label = 0 - } -// A triple where the subject is a chemical and the object is a disease. -message ChemicalToDiseaseRelationship - { - string qualifier = 0 - chemical subject = 0 - disease object = 0 - chemicalToDiseasePredicate predicate = 0 - namedEntity subjectQualifier = 0 - namedEntity objectQualifier = 0 - } -message Disease - { - string label = 0 - string id = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/ctd/shacl/ctd.shacl.ttl b/projects/ctd/shacl/ctd.shacl.ttl deleted file mode 100644 index 9dd8fa86c..000000000 --- a/projects/ctd/shacl/ctd.shacl.ttl +++ /dev/null @@ -1,264 +0,0 @@ -@prefix drug: <http://w3id.org/ontogpt/drug/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -drug:ChemicalToDiseaseDocument a sh:NodeShape ; - sh:closed true ; - sh:description "A document that contains chemical to disease relations." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class drug:ChemicalToDiseaseRelationship ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass drug:ChemicalToDiseaseDocument . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -drug:Chemical a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ; - sh:pattern "^MESH:[CD][0-9]{6}$" ] ; - sh:targetClass drug:Chemical . - -drug:ChemicalToDiseasePredicate a sh:NodeShape ; - sh:closed true ; - sh:description "A predicate for chemical to disease relationships" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass drug:ChemicalToDiseasePredicate . - -drug:ChemicalToDiseaseRelationship a sh:NodeShape ; - sh:closed true ; - sh:description "A triple where the subject is a chemical and the object is a disease." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the chemical, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class drug:Disease ; - sh:description "The disease or condition that is being treated or induced by the chemical. For example, asthma, cancer, covid-19, cardiac asystole, Hypotension, Headache." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class drug:ChemicalToDiseasePredicate ; - sh:description "The relationship type, e.g. INDUCES, TREATS." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class drug:Chemical ; - sh:description "The chemical substance, drug, or small molecule. For example: Lidocaine, Monosodium Glutamate, Imatinib." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the disease, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ] ; - sh:targetClass drug:ChemicalToDiseaseRelationship . - -drug:Disease a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ; - sh:pattern "^MESH:[CD][0-9]{6}$" ] ; - sh:targetClass drug:Disease . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/ctd/shex/ctd.shex b/projects/ctd/shex/ctd.shex deleted file mode 100644 index 89f380355..000000000 --- a/projects/ctd/shex/ctd.shex +++ /dev/null @@ -1,186 +0,0 @@ -BASE <http://w3id.org/ontogpt/drug/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<Chemical> CLOSED { - ( $<Chemical_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Chemical> ] - ) -} - -<ChemicalToDiseaseDocument> CLOSED { - ( $<ChemicalToDiseaseDocument_tes> ( &core:TextWithTriples_tes ; - rdf:type [ core:TextWithTriples ] ? ; - <triples> @<ChemicalToDiseaseRelationship> * - ) ; - rdf:type [ <ChemicalToDiseaseDocument> ] ? - ) -} - -<ChemicalToDiseasePredicate> CLOSED { - ( $<ChemicalToDiseasePredicate_tes> ( &core:RelationshipType_tes ; - rdf:type [ core:RelationshipType ] ? - ) ; - rdf:type [ <ChemicalToDiseasePredicate> ] - ) -} - -<ChemicalToDiseaseRelationship> CLOSED { - ( $<ChemicalToDiseaseRelationship_tes> ( &core:Triple_tes ; - rdf:type [ core:Triple ] ? ; - <subject> @<Chemical> ? ; - <object> @<Disease> ? ; - <predicate> @<ChemicalToDiseasePredicate> ? ; - <subject_qualifier> @core:NamedEntity ? ; - <object_qualifier> @core:NamedEntity ? - ) ; - rdf:type [ <ChemicalToDiseaseRelationship> ] ? - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -<Disease> CLOSED { - ( $<Disease_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Disease> ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -core:NamedEntity ( - @<Chemical> OR @<Disease> OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType ( - CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) - } OR @<ChemicalToDiseasePredicate> -) - -core:TextWithTriples ( - CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) - } OR @<ChemicalToDiseaseDocument> -) - -core:Triple ( - { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) - } OR @<ChemicalToDiseaseRelationship> -) - - diff --git a/projects/ctd/sqlschema/ctd.sql b/projects/ctd/sqlschema/ctd.sql deleted file mode 100644 index c460b2ab7..000000000 --- a/projects/ctd/sqlschema/ctd.sql +++ /dev/null @@ -1,77 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Chemical" ( - label TEXT, - id TEXT NOT NULL, - PRIMARY KEY (id) -); - -CREATE TABLE "ChemicalToDiseaseDocument" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "ChemicalToDiseasePredicate" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Disease" ( - label TEXT, - id TEXT NOT NULL, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "ChemicalToDiseaseRelationship" ( - qualifier TEXT, - subject TEXT, - object TEXT, - predicate TEXT, - subject_qualifier TEXT, - object_qualifier TEXT, - PRIMARY KEY (qualifier, subject, object, predicate, subject_qualifier, object_qualifier), - FOREIGN KEY(subject) REFERENCES "Chemical" (id), - FOREIGN KEY(object) REFERENCES "Disease" (id), - FOREIGN KEY(predicate) REFERENCES "ChemicalToDiseasePredicate" (id) -); diff --git a/projects/diagnostic_procedure/diagnostic_procedure.py b/projects/diagnostic_procedure/diagnostic_procedure.py deleted file mode 100644 index fc07e9b51..000000000 --- a/projects/diagnostic_procedure/diagnostic_procedure.py +++ /dev/null @@ -1,658 +0,0 @@ -# Auto generated from diagnostic_procedure.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:52:38 -# Schema: diagnostic_procedure -# -# id: http://w3id.org/ontogpt/diagnostic_procedure -# description: A template for clinical diagnostic procedures and the phenotypes they may contribute to. -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -HP = CurieNamespace('HP', 'http://purl.obolibrary.org/obo/HP_') -LOINC = CurieNamespace('LOINC', 'http://loinc.org/rdf/') -OBA = CurieNamespace('OBA', 'http://purl.obolibrary.org/obo/OBA_') -PATO = CurieNamespace('PATO', 'http://purl.obolibrary.org/obo/PATO_') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -UO = CurieNamespace('UO', 'http://example.org/UNKNOWN/UO/') -BIOLINK = CurieNamespace('biolink', 'https://w3id.org/biolink/vocab/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -DIAG = CurieNamespace('diag', 'http://w3id.org/ontogpt/diagnostic_procedure/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = DIAG - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class DiagnosticProcedureId(NamedEntityId): - pass - - -class PhenotypeId(NamedEntityId): - pass - - -class ClinicalAttributeId(NamedEntityId): - pass - - -class QualityId(NamedEntityId): - pass - - -class UnitId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -class ProcedureToPhenotypePredicateId(RelationshipTypeId): - pass - - -class ProcedureToAttributePredicateId(RelationshipTypeId): - pass - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = DIAG.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = DIAG.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class DiagnosticProcedure(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.DiagnosticProcedure - class_class_curie: ClassVar[str] = "diag:DiagnosticProcedure" - class_name: ClassVar[str] = "DiagnosticProcedure" - class_model_uri: ClassVar[URIRef] = DIAG.DiagnosticProcedure - - id: Union[str, DiagnosticProcedureId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiagnosticProcedureId): - self.id = DiagnosticProcedureId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Phenotype(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.Phenotype - class_class_curie: ClassVar[str] = "diag:Phenotype" - class_name: ClassVar[str] = "Phenotype" - class_model_uri: ClassVar[URIRef] = DIAG.Phenotype - - id: Union[str, PhenotypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PhenotypeId): - self.id = PhenotypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ClinicalAttribute(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.ClinicalAttribute - class_class_curie: ClassVar[str] = "diag:ClinicalAttribute" - class_name: ClassVar[str] = "ClinicalAttribute" - class_model_uri: ClassVar[URIRef] = DIAG.ClinicalAttribute - - id: Union[str, ClinicalAttributeId] = None - unit: Optional[Union[str, UnitId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ClinicalAttributeId): - self.id = ClinicalAttributeId(self.id) - - if self.unit is not None and not isinstance(self.unit, UnitId): - self.unit = UnitId(self.unit) - - super().__post_init__(**kwargs) - - -@dataclass -class Quality(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.Quality - class_class_curie: ClassVar[str] = "diag:Quality" - class_name: ClassVar[str] = "Quality" - class_model_uri: ClassVar[URIRef] = DIAG.Quality - - id: Union[str, QualityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, QualityId): - self.id = QualityId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Unit(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.Unit - class_class_curie: ClassVar[str] = "diag:Unit" - class_name: ClassVar[str] = "Unit" - class_model_uri: ClassVar[URIRef] = DIAG.Unit - - id: Union[str, UnitId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, UnitId): - self.id = UnitId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = DIAG.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = DIAG.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class DiagnosticProceduretoPhenotypeAssociation(Triple): - """ - A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., "blood - pressure measurement" is associated with "high blood pressure". - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.DiagnosticProceduretoPhenotypeAssociation - class_class_curie: ClassVar[str] = "diag:DiagnosticProceduretoPhenotypeAssociation" - class_name: ClassVar[str] = "DiagnosticProceduretoPhenotypeAssociation" - class_model_uri: ClassVar[URIRef] = DIAG.DiagnosticProceduretoPhenotypeAssociation - - subject: Optional[Union[str, DiagnosticProcedureId]] = None - object: Optional[Union[Union[str, PhenotypeId], List[Union[str, PhenotypeId]]]] = empty_list() - predicate: Optional[Union[str, ProcedureToPhenotypePredicateId]] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, DiagnosticProcedureId): - self.subject = DiagnosticProcedureId(self.subject) - - if not isinstance(self.object, list): - self.object = [self.object] if self.object is not None else [] - self.object = [v if isinstance(v, PhenotypeId) else PhenotypeId(v) for v in self.object] - - if self.predicate is not None and not isinstance(self.predicate, ProcedureToPhenotypePredicateId): - self.predicate = ProcedureToPhenotypePredicateId(self.predicate) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class DiagnosticProceduretoAttributeAssociation(Triple): - """ - A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., "blood - pressure measurement" is associated with "blood pressure" (or in OBA, something like OBA:VT0000183, "blood - pressure trait"). - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.DiagnosticProceduretoAttributeAssociation - class_class_curie: ClassVar[str] = "diag:DiagnosticProceduretoAttributeAssociation" - class_name: ClassVar[str] = "DiagnosticProceduretoAttributeAssociation" - class_model_uri: ClassVar[URIRef] = DIAG.DiagnosticProceduretoAttributeAssociation - - subject: Optional[Union[str, DiagnosticProcedureId]] = None - object: Optional[Union[Union[str, ClinicalAttributeId], List[Union[str, ClinicalAttributeId]]]] = empty_list() - predicate: Optional[Union[str, ProcedureToAttributePredicateId]] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, QualityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, DiagnosticProcedureId): - self.subject = DiagnosticProcedureId(self.subject) - - if not isinstance(self.object, list): - self.object = [self.object] if self.object is not None else [] - self.object = [v if isinstance(v, ClinicalAttributeId) else ClinicalAttributeId(v) for v in self.object] - - if self.predicate is not None and not isinstance(self.predicate, ProcedureToAttributePredicateId): - self.predicate = ProcedureToAttributePredicateId(self.predicate) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, QualityId): - self.object_qualifier = QualityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = DIAG.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = DIAG.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ProcedureToPhenotypePredicate(RelationshipType): - """ - A predicate for procedure to phenotype relationships, defining "this procedure is intended to provide support - for/against this phenotype". - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.ProcedureToPhenotypePredicate - class_class_curie: ClassVar[str] = "diag:ProcedureToPhenotypePredicate" - class_name: ClassVar[str] = "ProcedureToPhenotypePredicate" - class_model_uri: ClassVar[URIRef] = DIAG.ProcedureToPhenotypePredicate - - id: Union[str, ProcedureToPhenotypePredicateId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ProcedureToPhenotypePredicateId): - self.id = ProcedureToPhenotypePredicateId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ProcedureToAttributePredicate(RelationshipType): - """ - A predicate for procedure to attribute relationships, defining "this procedure is a measurement of this attribute". - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DIAG.ProcedureToAttributePredicate - class_class_curie: ClassVar[str] = "diag:ProcedureToAttributePredicate" - class_name: ClassVar[str] = "ProcedureToAttributePredicate" - class_model_uri: ClassVar[URIRef] = DIAG.ProcedureToAttributePredicate - - id: Union[str, ProcedureToAttributePredicateId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ProcedureToAttributePredicateId): - self.id = ProcedureToAttributePredicateId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = DIAG.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = DIAG.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.clinicalAttribute__unit = Slot(uri=DIAG.unit, name="clinicalAttribute__unit", curie=DIAG.curie('unit'), - model_uri=DIAG.clinicalAttribute__unit, domain=None, range=Optional[Union[str, UnitId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=DIAG.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=DIAG.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=DIAG.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=DIAG.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=DIAG.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=DIAG.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=DIAG.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=DIAG.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=DIAG.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=DIAG.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=DIAG.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=DIAG.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=DIAG.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=DIAG.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=DIAG.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=DIAG.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=DIAG.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=DIAG.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=DIAG.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=DIAG.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=DIAG.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=DIAG.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=DIAG.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=DIAG.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=DIAG.annotatorResult__object_text, domain=None, range=Optional[str]) - -slots.DiagnosticProceduretoPhenotypeAssociation_subject = Slot(uri=DIAG.subject, name="DiagnosticProceduretoPhenotypeAssociation_subject", curie=DIAG.curie('subject'), - model_uri=DIAG.DiagnosticProceduretoPhenotypeAssociation_subject, domain=DiagnosticProceduretoPhenotypeAssociation, range=Optional[Union[str, DiagnosticProcedureId]]) - -slots.DiagnosticProceduretoPhenotypeAssociation_object = Slot(uri=DIAG.object, name="DiagnosticProceduretoPhenotypeAssociation_object", curie=DIAG.curie('object'), - model_uri=DIAG.DiagnosticProceduretoPhenotypeAssociation_object, domain=DiagnosticProceduretoPhenotypeAssociation, range=Optional[Union[Union[str, PhenotypeId], List[Union[str, PhenotypeId]]]]) - -slots.DiagnosticProceduretoPhenotypeAssociation_predicate = Slot(uri=DIAG.predicate, name="DiagnosticProceduretoPhenotypeAssociation_predicate", curie=DIAG.curie('predicate'), - model_uri=DIAG.DiagnosticProceduretoPhenotypeAssociation_predicate, domain=DiagnosticProceduretoPhenotypeAssociation, range=Optional[Union[str, ProcedureToPhenotypePredicateId]]) - -slots.DiagnosticProceduretoPhenotypeAssociation_subject_qualifier = Slot(uri=DIAG.subject_qualifier, name="DiagnosticProceduretoPhenotypeAssociation_subject_qualifier", curie=DIAG.curie('subject_qualifier'), - model_uri=DIAG.DiagnosticProceduretoPhenotypeAssociation_subject_qualifier, domain=DiagnosticProceduretoPhenotypeAssociation, range=Optional[Union[str, NamedEntityId]]) - -slots.DiagnosticProceduretoPhenotypeAssociation_object_qualifier = Slot(uri=DIAG.object_qualifier, name="DiagnosticProceduretoPhenotypeAssociation_object_qualifier", curie=DIAG.curie('object_qualifier'), - model_uri=DIAG.DiagnosticProceduretoPhenotypeAssociation_object_qualifier, domain=DiagnosticProceduretoPhenotypeAssociation, range=Optional[Union[str, NamedEntityId]]) - -slots.DiagnosticProceduretoAttributeAssociation_subject = Slot(uri=DIAG.subject, name="DiagnosticProceduretoAttributeAssociation_subject", curie=DIAG.curie('subject'), - model_uri=DIAG.DiagnosticProceduretoAttributeAssociation_subject, domain=DiagnosticProceduretoAttributeAssociation, range=Optional[Union[str, DiagnosticProcedureId]]) - -slots.DiagnosticProceduretoAttributeAssociation_object = Slot(uri=DIAG.object, name="DiagnosticProceduretoAttributeAssociation_object", curie=DIAG.curie('object'), - model_uri=DIAG.DiagnosticProceduretoAttributeAssociation_object, domain=DiagnosticProceduretoAttributeAssociation, range=Optional[Union[Union[str, ClinicalAttributeId], List[Union[str, ClinicalAttributeId]]]]) - -slots.DiagnosticProceduretoAttributeAssociation_predicate = Slot(uri=DIAG.predicate, name="DiagnosticProceduretoAttributeAssociation_predicate", curie=DIAG.curie('predicate'), - model_uri=DIAG.DiagnosticProceduretoAttributeAssociation_predicate, domain=DiagnosticProceduretoAttributeAssociation, range=Optional[Union[str, ProcedureToAttributePredicateId]]) - -slots.DiagnosticProceduretoAttributeAssociation_subject_qualifier = Slot(uri=DIAG.subject_qualifier, name="DiagnosticProceduretoAttributeAssociation_subject_qualifier", curie=DIAG.curie('subject_qualifier'), - model_uri=DIAG.DiagnosticProceduretoAttributeAssociation_subject_qualifier, domain=DiagnosticProceduretoAttributeAssociation, range=Optional[Union[str, NamedEntityId]]) - -slots.DiagnosticProceduretoAttributeAssociation_object_qualifier = Slot(uri=DIAG.object_qualifier, name="DiagnosticProceduretoAttributeAssociation_object_qualifier", curie=DIAG.curie('object_qualifier'), - model_uri=DIAG.DiagnosticProceduretoAttributeAssociation_object_qualifier, domain=DiagnosticProceduretoAttributeAssociation, range=Optional[Union[str, QualityId]]) \ No newline at end of file diff --git a/projects/diagnostic_procedure/docs/AnnotatorResult.md b/projects/diagnostic_procedure/docs/AnnotatorResult.md deleted file mode 100644 index 9123f01ac..000000000 --- a/projects/diagnostic_procedure/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [diag:AnnotatorResult](http://w3id.org/ontogpt/diagnostic_procedure/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/Any.md b/projects/diagnostic_procedure/docs/Any.md deleted file mode 100644 index 198c529ab..000000000 --- a/projects/diagnostic_procedure/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [diag:Any](http://w3id.org/ontogpt/diagnostic_procedure/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/diagnostic_procedure/docs/ClinicalAttribute.md b/projects/diagnostic_procedure/docs/ClinicalAttribute.md deleted file mode 100644 index a1ebe4855..000000000 --- a/projects/diagnostic_procedure/docs/ClinicalAttribute.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: ClinicalAttribute - - - - -URI: [diag:ClinicalAttribute](http://w3id.org/ontogpt/diagnostic_procedure/ClinicalAttribute) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[NamedEntity],[DiagnosticProceduretoAttributeAssociation],[Unit]<unit%200..1-%20[ClinicalAttribute|id(i):string;label(i):string%20%3F],[DiagnosticProceduretoAttributeAssociation]-%20object%200..*>[ClinicalAttribute],[NamedEntity]^-[ClinicalAttribute])](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[NamedEntity],[DiagnosticProceduretoAttributeAssociation],[Unit]<unit%200..1-%20[ClinicalAttribute|id(i):string;label(i):string%20%3F],[DiagnosticProceduretoAttributeAssociation]-%20object%200..*>[ClinicalAttribute],[NamedEntity]^-[ClinicalAttribute]) - -## Identifier prefixes - - * OBA - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md)** *[DiagnosticProceduretoAttributeAssociation➞object](DiagnosticProceduretoAttributeAssociation_object.md)* <sub>0..\*</sub> **[ClinicalAttribute](ClinicalAttribute.md)** - -## Attributes - - -### Own - - * [➞unit](clinicalAttribute__unit.md) <sub>0..1</sub> - * Description: the unit used to measure the attribute - * Range: [Unit](Unit.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/CompoundExpression.md b/projects/diagnostic_procedure/docs/CompoundExpression.md deleted file mode 100644 index ceff89418..000000000 --- a/projects/diagnostic_procedure/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [diag:CompoundExpression](http://w3id.org/ontogpt/diagnostic_procedure/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/diagnostic_procedure/docs/DiagnosticProcedure.md b/projects/diagnostic_procedure/docs/DiagnosticProcedure.md deleted file mode 100644 index 117f9269d..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProcedure.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: DiagnosticProcedure - - - - -URI: [diag:DiagnosticProcedure](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProcedure) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProceduretoAttributeAssociation],[DiagnosticProceduretoAttributeAssociation]-%20subject%200..1>[DiagnosticProcedure|id(i):string;label(i):string%20%3F],[DiagnosticProceduretoPhenotypeAssociation]-%20subject%200..1>[DiagnosticProcedure],[NamedEntity]^-[DiagnosticProcedure])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProceduretoAttributeAssociation],[DiagnosticProceduretoAttributeAssociation]-%20subject%200..1>[DiagnosticProcedure|id(i):string;label(i):string%20%3F],[DiagnosticProceduretoPhenotypeAssociation]-%20subject%200..1>[DiagnosticProcedure],[NamedEntity]^-[DiagnosticProcedure]) - -## Identifier prefixes - - * LOINC - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md)** *[DiagnosticProceduretoAttributeAssociation➞subject](DiagnosticProceduretoAttributeAssociation_subject.md)* <sub>0..1</sub> **[DiagnosticProcedure](DiagnosticProcedure.md)** - * **[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md)** *[DiagnosticProceduretoPhenotypeAssociation➞subject](DiagnosticProceduretoPhenotypeAssociation_subject.md)* <sub>0..1</sub> **[DiagnosticProcedure](DiagnosticProcedure.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation.md deleted file mode 100644 index 73abb979d..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation.md +++ /dev/null @@ -1,44 +0,0 @@ - -# Class: DiagnosticProceduretoAttributeAssociation - - -A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., "blood pressure measurement" is associated with "blood pressure" (or in OBA, something like OBA:VT0000183, "blood pressure trait"). - -URI: [diag:DiagnosticProceduretoAttributeAssociation](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoAttributeAssociation) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Quality],[ProcedureToAttributePredicate],[NamedEntity],[Quality]<object_qualifier%200..1-%20[DiagnosticProceduretoAttributeAssociation|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[DiagnosticProceduretoAttributeAssociation],[ProcedureToAttributePredicate]<predicate%200..1-%20[DiagnosticProceduretoAttributeAssociation],[ClinicalAttribute]<object%200..*-%20[DiagnosticProceduretoAttributeAssociation],[DiagnosticProcedure]<subject%200..1-%20[DiagnosticProceduretoAttributeAssociation],[Triple]^-[DiagnosticProceduretoAttributeAssociation],[DiagnosticProcedure],[ClinicalAttribute])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Quality],[ProcedureToAttributePredicate],[NamedEntity],[Quality]<object_qualifier%200..1-%20[DiagnosticProceduretoAttributeAssociation|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[DiagnosticProceduretoAttributeAssociation],[ProcedureToAttributePredicate]<predicate%200..1-%20[DiagnosticProceduretoAttributeAssociation],[ClinicalAttribute]<object%200..*-%20[DiagnosticProceduretoAttributeAssociation],[DiagnosticProcedure]<subject%200..1-%20[DiagnosticProceduretoAttributeAssociation],[Triple]^-[DiagnosticProceduretoAttributeAssociation],[DiagnosticProcedure],[ClinicalAttribute]) - -## Parents - - * is_a: [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - - -### Own - - * [DiagnosticProceduretoAttributeAssociation➞subject](DiagnosticProceduretoAttributeAssociation_subject.md) <sub>0..1</sub> - * Description: A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include "heart rate measurement", "blood pressure measurement", "oxygen saturation measurement", etc. In practice, procedures may be named based on what they measure, with the "measurement" part left implicit. - * Range: [DiagnosticProcedure](DiagnosticProcedure.md) - * [DiagnosticProceduretoAttributeAssociation➞object](DiagnosticProceduretoAttributeAssociation_object.md) <sub>0..\*</sub> - * Description: Any measurable clinical attribute. - * Range: [ClinicalAttribute](ClinicalAttribute.md) - * [DiagnosticProceduretoAttributeAssociation➞predicate](DiagnosticProceduretoAttributeAssociation_predicate.md) <sub>0..1</sub> - * Description: The relationship type, e.g. RELATED_TO - * Range: [ProcedureToAttributePredicate](ProcedureToAttributePredicate.md) - * [DiagnosticProceduretoAttributeAssociation➞subject_qualifier](DiagnosticProceduretoAttributeAssociation_subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the procedure. - * Range: [NamedEntity](NamedEntity.md) - * [DiagnosticProceduretoAttributeAssociation➞object_qualifier](DiagnosticProceduretoAttributeAssociation_object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the phenotype. - * Range: [Quality](Quality.md) - -### Inherited from Triple: - - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_object.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_object.md deleted file mode 100644 index 03a929c8a..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_object.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object - - -Any measurable clinical attribute. - -URI: [diag:DiagnosticProceduretoAttributeAssociation_object](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoAttributeAssociation_object) - - -## Domain and Range - -[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) → <sub>0..\*</sub> [ClinicalAttribute](ClinicalAttribute.md) - -## Parents - - * is_a: [➞object](triple__object.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_object_qualifier.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_object_qualifier.md deleted file mode 100644 index 811c766fa..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_object_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the phenotype. - -URI: [diag:DiagnosticProceduretoAttributeAssociation_object_qualifier](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoAttributeAssociation_object_qualifier) - - -## Domain and Range - -[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) → <sub>0..1</sub> [Quality](Quality.md) - -## Parents - - * is_a: [➞object_qualifier](triple__object_qualifier.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_predicate.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_predicate.md deleted file mode 100644 index 3ddf05152..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_predicate.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: predicate - - -The relationship type, e.g. RELATED_TO - -URI: [diag:DiagnosticProceduretoAttributeAssociation_predicate](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoAttributeAssociation_predicate) - - -## Domain and Range - -[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) → <sub>0..1</sub> [ProcedureToAttributePredicate](ProcedureToAttributePredicate.md) - -## Parents - - * is_a: [➞predicate](triple__predicate.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_subject.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_subject.md deleted file mode 100644 index fcb44273f..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_subject.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject - - -A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include "heart rate measurement", "blood pressure measurement", "oxygen saturation measurement", etc. In practice, procedures may be named based on what they measure, with the "measurement" part left implicit. - -URI: [diag:DiagnosticProceduretoAttributeAssociation_subject](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoAttributeAssociation_subject) - - -## Domain and Range - -[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) → <sub>0..1</sub> [DiagnosticProcedure](DiagnosticProcedure.md) - -## Parents - - * is_a: [➞subject](triple__subject.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_subject_qualifier.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_subject_qualifier.md deleted file mode 100644 index 8554c92e1..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoAttributeAssociation_subject_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the procedure. - -URI: [diag:DiagnosticProceduretoAttributeAssociation_subject_qualifier](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoAttributeAssociation_subject_qualifier) - - -## Domain and Range - -[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞subject_qualifier](triple__subject_qualifier.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation.md deleted file mode 100644 index 13a206e17..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation.md +++ /dev/null @@ -1,44 +0,0 @@ - -# Class: DiagnosticProceduretoPhenotypeAssociation - - -A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., "blood pressure measurement" is associated with "high blood pressure". - -URI: [diag:DiagnosticProceduretoPhenotypeAssociation](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[ProcedureToPhenotypePredicate],[Phenotype],[NamedEntity],[NamedEntity]<object_qualifier%200..1-%20[DiagnosticProceduretoPhenotypeAssociation|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[DiagnosticProceduretoPhenotypeAssociation],[ProcedureToPhenotypePredicate]<predicate%200..1-%20[DiagnosticProceduretoPhenotypeAssociation],[Phenotype]<object%200..*-%20[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProcedure]<subject%200..1-%20[DiagnosticProceduretoPhenotypeAssociation],[Triple]^-[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProcedure])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[ProcedureToPhenotypePredicate],[Phenotype],[NamedEntity],[NamedEntity]<object_qualifier%200..1-%20[DiagnosticProceduretoPhenotypeAssociation|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[DiagnosticProceduretoPhenotypeAssociation],[ProcedureToPhenotypePredicate]<predicate%200..1-%20[DiagnosticProceduretoPhenotypeAssociation],[Phenotype]<object%200..*-%20[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProcedure]<subject%200..1-%20[DiagnosticProceduretoPhenotypeAssociation],[Triple]^-[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProcedure]) - -## Parents - - * is_a: [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - - -### Own - - * [DiagnosticProceduretoPhenotypeAssociation➞subject](DiagnosticProceduretoPhenotypeAssociation_subject.md) <sub>0..1</sub> - * Description: A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include "heart rate measurement", "blood pressure measurement", "oxygen saturation measurement", etc. In practice, procedures may be named based on what they measure, with the "measurement" part left implicit. - * Range: [DiagnosticProcedure](DiagnosticProcedure.md) - * [DiagnosticProceduretoPhenotypeAssociation➞object](DiagnosticProceduretoPhenotypeAssociation_object.md) <sub>0..\*</sub> - * Description: The observable physical or biochemical characteristics of a patient. Not equivalent to a disease state, but may contribute to a diagnosis. - * Range: [Phenotype](Phenotype.md) - * [DiagnosticProceduretoPhenotypeAssociation➞predicate](DiagnosticProceduretoPhenotypeAssociation_predicate.md) <sub>0..1</sub> - * Description: The relationship type, e.g. RELATED_TO - * Range: [ProcedureToPhenotypePredicate](ProcedureToPhenotypePredicate.md) - * [DiagnosticProceduretoPhenotypeAssociation➞subject_qualifier](DiagnosticProceduretoPhenotypeAssociation_subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the procedure. - * Range: [NamedEntity](NamedEntity.md) - * [DiagnosticProceduretoPhenotypeAssociation➞object_qualifier](DiagnosticProceduretoPhenotypeAssociation_object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the phenotype. - * Range: [NamedEntity](NamedEntity.md) - -### Inherited from Triple: - - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_object.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_object.md deleted file mode 100644 index 3aa84aeef..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_object.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object - - -The observable physical or biochemical characteristics of a patient. Not equivalent to a disease state, but may contribute to a diagnosis. - -URI: [diag:DiagnosticProceduretoPhenotypeAssociation_object](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation_object) - - -## Domain and Range - -[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) → <sub>0..\*</sub> [Phenotype](Phenotype.md) - -## Parents - - * is_a: [➞object](triple__object.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_object_qualifier.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_object_qualifier.md deleted file mode 100644 index cc6d50b0a..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_object_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the phenotype. - -URI: [diag:DiagnosticProceduretoPhenotypeAssociation_object_qualifier](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation_object_qualifier) - - -## Domain and Range - -[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞object_qualifier](triple__object_qualifier.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_predicate.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_predicate.md deleted file mode 100644 index aa7230fd3..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_predicate.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: predicate - - -The relationship type, e.g. RELATED_TO - -URI: [diag:DiagnosticProceduretoPhenotypeAssociation_predicate](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation_predicate) - - -## Domain and Range - -[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) → <sub>0..1</sub> [ProcedureToPhenotypePredicate](ProcedureToPhenotypePredicate.md) - -## Parents - - * is_a: [➞predicate](triple__predicate.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_subject.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_subject.md deleted file mode 100644 index 5fc29c421..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_subject.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject - - -A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include "heart rate measurement", "blood pressure measurement", "oxygen saturation measurement", etc. In practice, procedures may be named based on what they measure, with the "measurement" part left implicit. - -URI: [diag:DiagnosticProceduretoPhenotypeAssociation_subject](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation_subject) - - -## Domain and Range - -[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) → <sub>0..1</sub> [DiagnosticProcedure](DiagnosticProcedure.md) - -## Parents - - * is_a: [➞subject](triple__subject.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_subject_qualifier.md b/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_subject_qualifier.md deleted file mode 100644 index 705e762d7..000000000 --- a/projects/diagnostic_procedure/docs/DiagnosticProceduretoPhenotypeAssociation_subject_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the procedure. - -URI: [diag:DiagnosticProceduretoPhenotypeAssociation_subject_qualifier](http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation_subject_qualifier) - - -## Domain and Range - -[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞subject_qualifier](triple__subject_qualifier.md) - -## Children - - -## Used by - - * [DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) diff --git a/projects/diagnostic_procedure/docs/ExtractionResult.md b/projects/diagnostic_procedure/docs/ExtractionResult.md deleted file mode 100644 index d0c5a25fc..000000000 --- a/projects/diagnostic_procedure/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [diag:ExtractionResult](http://w3id.org/ontogpt/diagnostic_procedure/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/diagnostic_procedure/docs/NamedEntity.md b/projects/diagnostic_procedure/docs/NamedEntity.md deleted file mode 100644 index 62b033567..000000000 --- a/projects/diagnostic_procedure/docs/NamedEntity.md +++ /dev/null @@ -1,41 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [diag:NamedEntity](http://w3id.org/ontogpt/diagnostic_procedure/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[RelationshipType],[Quality],[Phenotype],[DiagnosticProceduretoAttributeAssociation]-%20subject_qualifier%200..1>[NamedEntity|id:string;label:string%20%3F],[DiagnosticProceduretoPhenotypeAssociation]-%20object_qualifier%200..1>[NamedEntity],[DiagnosticProceduretoPhenotypeAssociation]-%20subject_qualifier%200..1>[NamedEntity],[Triple]-%20object%200..1>[NamedEntity],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Unit],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Quality],[NamedEntity]^-[Phenotype],[NamedEntity]^-[DiagnosticProcedure],[NamedEntity]^-[ClinicalAttribute],[Triple],[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProceduretoAttributeAssociation],[DiagnosticProcedure],[ClinicalAttribute])](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[RelationshipType],[Quality],[Phenotype],[DiagnosticProceduretoAttributeAssociation]-%20subject_qualifier%200..1>[NamedEntity|id:string;label:string%20%3F],[DiagnosticProceduretoPhenotypeAssociation]-%20object_qualifier%200..1>[NamedEntity],[DiagnosticProceduretoPhenotypeAssociation]-%20subject_qualifier%200..1>[NamedEntity],[Triple]-%20object%200..1>[NamedEntity],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Unit],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Quality],[NamedEntity]^-[Phenotype],[NamedEntity]^-[DiagnosticProcedure],[NamedEntity]^-[ClinicalAttribute],[Triple],[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProceduretoAttributeAssociation],[DiagnosticProcedure],[ClinicalAttribute]) - -## Children - - * [ClinicalAttribute](ClinicalAttribute.md) - * [DiagnosticProcedure](DiagnosticProcedure.md) - * [Phenotype](Phenotype.md) - * [Quality](Quality.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - -## Referenced by Class - - * **[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md)** *[DiagnosticProceduretoAttributeAssociation➞subject_qualifier](DiagnosticProceduretoAttributeAssociation_subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md)** *[DiagnosticProceduretoPhenotypeAssociation➞object_qualifier](DiagnosticProceduretoPhenotypeAssociation_object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md)** *[DiagnosticProceduretoPhenotypeAssociation➞subject_qualifier](DiagnosticProceduretoPhenotypeAssociation_subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/NullDataOptions.md b/projects/diagnostic_procedure/docs/NullDataOptions.md deleted file mode 100644 index d738f531e..000000000 --- a/projects/diagnostic_procedure/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [diag:NullDataOptions](http://w3id.org/ontogpt/diagnostic_procedure/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/diagnostic_procedure/docs/Phenotype.md b/projects/diagnostic_procedure/docs/Phenotype.md deleted file mode 100644 index cf80c0771..000000000 --- a/projects/diagnostic_procedure/docs/Phenotype.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Phenotype - - - - -URI: [diag:Phenotype](http://w3id.org/ontogpt/diagnostic_procedure/Phenotype) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[DiagnosticProceduretoPhenotypeAssociation]-%20object%200..*>[Phenotype|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Phenotype],[NamedEntity],[DiagnosticProceduretoPhenotypeAssociation])](https://yuml.me/diagram/nofunky;dir:TB/class/[DiagnosticProceduretoPhenotypeAssociation]-%20object%200..*>[Phenotype|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Phenotype],[NamedEntity],[DiagnosticProceduretoPhenotypeAssociation]) - -## Identifier prefixes - - * HP - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md)** *[DiagnosticProceduretoPhenotypeAssociation➞object](DiagnosticProceduretoPhenotypeAssociation_object.md)* <sub>0..\*</sub> **[Phenotype](Phenotype.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/ProcedureToAttributePredicate.md b/projects/diagnostic_procedure/docs/ProcedureToAttributePredicate.md deleted file mode 100644 index a7476bca7..000000000 --- a/projects/diagnostic_procedure/docs/ProcedureToAttributePredicate.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: ProcedureToAttributePredicate - - -A predicate for procedure to attribute relationships, defining "this procedure is a measurement of this attribute". - -URI: [diag:ProcedureToAttributePredicate](http://w3id.org/ontogpt/diagnostic_procedure/ProcedureToAttributePredicate) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[DiagnosticProceduretoAttributeAssociation]-%20predicate%200..1>[ProcedureToAttributePredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ProcedureToAttributePredicate],[DiagnosticProceduretoAttributeAssociation])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[DiagnosticProceduretoAttributeAssociation]-%20predicate%200..1>[ProcedureToAttributePredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ProcedureToAttributePredicate],[DiagnosticProceduretoAttributeAssociation]) - -## Parents - - * is_a: [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md)** *[DiagnosticProceduretoAttributeAssociation➞predicate](DiagnosticProceduretoAttributeAssociation_predicate.md)* <sub>0..1</sub> **[ProcedureToAttributePredicate](ProcedureToAttributePredicate.md)** - -## Attributes - - -### Inherited from RelationshipType: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/ProcedureToPhenotypePredicate.md b/projects/diagnostic_procedure/docs/ProcedureToPhenotypePredicate.md deleted file mode 100644 index 98caa15f3..000000000 --- a/projects/diagnostic_procedure/docs/ProcedureToPhenotypePredicate.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: ProcedureToPhenotypePredicate - - -A predicate for procedure to phenotype relationships, defining "this procedure is intended to provide support for/against this phenotype". - -URI: [diag:ProcedureToPhenotypePredicate](http://w3id.org/ontogpt/diagnostic_procedure/ProcedureToPhenotypePredicate) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[DiagnosticProceduretoPhenotypeAssociation]-%20predicate%200..1>[ProcedureToPhenotypePredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ProcedureToPhenotypePredicate],[DiagnosticProceduretoPhenotypeAssociation])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[DiagnosticProceduretoPhenotypeAssociation]-%20predicate%200..1>[ProcedureToPhenotypePredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ProcedureToPhenotypePredicate],[DiagnosticProceduretoPhenotypeAssociation]) - -## Parents - - * is_a: [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **[DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md)** *[DiagnosticProceduretoPhenotypeAssociation➞predicate](DiagnosticProceduretoPhenotypeAssociation_predicate.md)* <sub>0..1</sub> **[ProcedureToPhenotypePredicate](ProcedureToPhenotypePredicate.md)** - -## Attributes - - -### Inherited from RelationshipType: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/Publication.md b/projects/diagnostic_procedure/docs/Publication.md deleted file mode 100644 index e43e6814e..000000000 --- a/projects/diagnostic_procedure/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [diag:Publication](http://w3id.org/ontogpt/diagnostic_procedure/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/Quality.md b/projects/diagnostic_procedure/docs/Quality.md deleted file mode 100644 index f8f84ec4b..000000000 --- a/projects/diagnostic_procedure/docs/Quality.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Quality - - - - -URI: [diag:Quality](http://w3id.org/ontogpt/diagnostic_procedure/Quality) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[DiagnosticProceduretoAttributeAssociation]-%20object_qualifier%200..1>[Quality|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Quality],[NamedEntity],[DiagnosticProceduretoAttributeAssociation])](https://yuml.me/diagram/nofunky;dir:TB/class/[DiagnosticProceduretoAttributeAssociation]-%20object_qualifier%200..1>[Quality|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Quality],[NamedEntity],[DiagnosticProceduretoAttributeAssociation]) - -## Identifier prefixes - - * PATO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md)** *[DiagnosticProceduretoAttributeAssociation➞object_qualifier](DiagnosticProceduretoAttributeAssociation_object_qualifier.md)* <sub>0..1</sub> **[Quality](Quality.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/RelationshipType.md b/projects/diagnostic_procedure/docs/RelationshipType.md deleted file mode 100644 index e5f7930cc..000000000 --- a/projects/diagnostic_procedure/docs/RelationshipType.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [diag:RelationshipType](http://w3id.org/ontogpt/diagnostic_procedure/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ProcedureToPhenotypePredicate],[RelationshipType]^-[ProcedureToAttributePredicate],[NamedEntity]^-[RelationshipType],[Triple],[ProcedureToPhenotypePredicate],[ProcedureToAttributePredicate],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ProcedureToPhenotypePredicate],[RelationshipType]^-[ProcedureToAttributePredicate],[NamedEntity]^-[RelationshipType],[Triple],[ProcedureToPhenotypePredicate],[ProcedureToAttributePredicate],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Children - - * [ProcedureToAttributePredicate](ProcedureToAttributePredicate.md) - A predicate for procedure to attribute relationships, defining "this procedure is a measurement of this attribute". - * [ProcedureToPhenotypePredicate](ProcedureToPhenotypePredicate.md) - A predicate for procedure to phenotype relationships, defining "this procedure is intended to provide support for/against this phenotype". - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/TextWithTriples.md b/projects/diagnostic_procedure/docs/TextWithTriples.md deleted file mode 100644 index 509967bdd..000000000 --- a/projects/diagnostic_procedure/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [diag:TextWithTriples](http://w3id.org/ontogpt/diagnostic_procedure/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/diagnostic_procedure/docs/Triple.md b/projects/diagnostic_procedure/docs/Triple.md deleted file mode 100644 index 999cbff06..000000000 --- a/projects/diagnostic_procedure/docs/Triple.md +++ /dev/null @@ -1,44 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [diag:Triple](http://w3id.org/ontogpt/diagnostic_procedure/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[Triple]^-[DiagnosticProceduretoPhenotypeAssociation],[Triple]^-[DiagnosticProceduretoAttributeAssociation],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProceduretoAttributeAssociation],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[Triple]^-[DiagnosticProceduretoPhenotypeAssociation],[Triple]^-[DiagnosticProceduretoAttributeAssociation],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[DiagnosticProceduretoPhenotypeAssociation],[DiagnosticProceduretoAttributeAssociation],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Children - - * [DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) - A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., "blood pressure measurement" is associated with "blood pressure" (or in OBA, something like OBA:VT0000183, "blood pressure trait"). - * [DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) - A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., "blood pressure measurement" is associated with "high blood pressure". - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/diagnostic_procedure/docs/Unit.md b/projects/diagnostic_procedure/docs/Unit.md deleted file mode 100644 index 9071553fc..000000000 --- a/projects/diagnostic_procedure/docs/Unit.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Unit - - - - -URI: [diag:Unit](http://w3id.org/ontogpt/diagnostic_procedure/Unit) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ClinicalAttribute]-%20unit%200..1>[Unit|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Unit],[NamedEntity],[ClinicalAttribute])](https://yuml.me/diagram/nofunky;dir:TB/class/[ClinicalAttribute]-%20unit%200..1>[Unit|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Unit],[NamedEntity],[ClinicalAttribute]) - -## Identifier prefixes - - * UO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞unit](clinicalAttribute__unit.md)* <sub>0..1</sub> **[Unit](Unit.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/diagnostic_procedure/docs/annotatorResult__object_id.md b/projects/diagnostic_procedure/docs/annotatorResult__object_id.md deleted file mode 100644 index e111af098..000000000 --- a/projects/diagnostic_procedure/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [diag:annotatorResult__object_id](http://w3id.org/ontogpt/diagnostic_procedure/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/diagnostic_procedure/docs/annotatorResult__object_text.md b/projects/diagnostic_procedure/docs/annotatorResult__object_text.md deleted file mode 100644 index 281f17ec2..000000000 --- a/projects/diagnostic_procedure/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [diag:annotatorResult__object_text](http://w3id.org/ontogpt/diagnostic_procedure/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/diagnostic_procedure/docs/annotatorResult__subject_text.md b/projects/diagnostic_procedure/docs/annotatorResult__subject_text.md deleted file mode 100644 index 715163dfa..000000000 --- a/projects/diagnostic_procedure/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [diag:annotatorResult__subject_text](http://w3id.org/ontogpt/diagnostic_procedure/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/diagnostic_procedure/docs/clinicalAttribute__unit.md b/projects/diagnostic_procedure/docs/clinicalAttribute__unit.md deleted file mode 100644 index 1963ae530..000000000 --- a/projects/diagnostic_procedure/docs/clinicalAttribute__unit.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: unit - - -the unit used to measure the attribute - -URI: [diag:clinicalAttribute__unit](http://w3id.org/ontogpt/diagnostic_procedure/clinicalAttribute__unit) - - -## Domain and Range - -None → <sub>0..1</sub> [Unit](Unit.md) - -## Parents - - -## Children - - -## Used by - - * [ClinicalAttribute](ClinicalAttribute.md) diff --git a/projects/diagnostic_procedure/docs/diagnostic_procedure.md b/projects/diagnostic_procedure/docs/diagnostic_procedure.md deleted file mode 100644 index 53ad1538d..000000000 --- a/projects/diagnostic_procedure/docs/diagnostic_procedure.md +++ /dev/null @@ -1,123 +0,0 @@ - -# diagnostic_procedure - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for clinical diagnostic procedures and the phenotypes they may contribute to. - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) - A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., "blood pressure measurement" is associated with "blood pressure" (or in OBA, something like OBA:VT0000183, "blood pressure trait"). - * [DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) - A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., "blood pressure measurement" is associated with "high blood pressure". - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [ClinicalAttribute](ClinicalAttribute.md) - * [DiagnosticProcedure](DiagnosticProcedure.md) - * [Phenotype](Phenotype.md) - * [Quality](Quality.md) - * [RelationshipType](RelationshipType.md) - * [ProcedureToAttributePredicate](ProcedureToAttributePredicate.md) - A predicate for procedure to attribute relationships, defining "this procedure is a measurement of this attribute". - * [ProcedureToPhenotypePredicate](ProcedureToPhenotypePredicate.md) - A predicate for procedure to phenotype relationships, defining "this procedure is intended to provide support for/against this phenotype". - * [Unit](Unit.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞unit](clinicalAttribute__unit.md) - the unit used to measure the attribute - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [DiagnosticProceduretoAttributeAssociation➞object](DiagnosticProceduretoAttributeAssociation_object.md) - Any measurable clinical attribute. - * [DiagnosticProceduretoPhenotypeAssociation➞object](DiagnosticProceduretoPhenotypeAssociation_object.md) - The observable physical or biochemical characteristics of a patient. Not equivalent to a disease state, but may contribute to a diagnosis. - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [DiagnosticProceduretoAttributeAssociation➞object_qualifier](DiagnosticProceduretoAttributeAssociation_object_qualifier.md) - An optional qualifier or modifier for the phenotype. - * [DiagnosticProceduretoPhenotypeAssociation➞object_qualifier](DiagnosticProceduretoPhenotypeAssociation_object_qualifier.md) - An optional qualifier or modifier for the phenotype. - * [➞predicate](triple__predicate.md) - * [DiagnosticProceduretoAttributeAssociation➞predicate](DiagnosticProceduretoAttributeAssociation_predicate.md) - The relationship type, e.g. RELATED_TO - * [DiagnosticProceduretoPhenotypeAssociation➞predicate](DiagnosticProceduretoPhenotypeAssociation_predicate.md) - The relationship type, e.g. RELATED_TO - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [DiagnosticProceduretoAttributeAssociation➞subject](DiagnosticProceduretoAttributeAssociation_subject.md) - A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include "heart rate measurement", "blood pressure measurement", "oxygen saturation measurement", etc. In practice, procedures may be named based on what they measure, with the "measurement" part left implicit. - * [DiagnosticProceduretoPhenotypeAssociation➞subject](DiagnosticProceduretoPhenotypeAssociation_subject.md) - A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include "heart rate measurement", "blood pressure measurement", "oxygen saturation measurement", etc. In practice, procedures may be named based on what they measure, with the "measurement" part left implicit. - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * [DiagnosticProceduretoAttributeAssociation➞subject_qualifier](DiagnosticProceduretoAttributeAssociation_subject_qualifier.md) - An optional qualifier or modifier for the procedure. - * [DiagnosticProceduretoPhenotypeAssociation➞subject_qualifier](DiagnosticProceduretoPhenotypeAssociation_subject_qualifier.md) - An optional qualifier or modifier for the procedure. - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/diagnostic_procedure/docs/extractionResult__extracted_object.md b/projects/diagnostic_procedure/docs/extractionResult__extracted_object.md deleted file mode 100644 index 030afba49..000000000 --- a/projects/diagnostic_procedure/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [diag:extractionResult__extracted_object](http://w3id.org/ontogpt/diagnostic_procedure/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/diagnostic_procedure/docs/extractionResult__input_id.md b/projects/diagnostic_procedure/docs/extractionResult__input_id.md deleted file mode 100644 index 4e5ce054c..000000000 --- a/projects/diagnostic_procedure/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [diag:extractionResult__input_id](http://w3id.org/ontogpt/diagnostic_procedure/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/diagnostic_procedure/docs/extractionResult__input_text.md b/projects/diagnostic_procedure/docs/extractionResult__input_text.md deleted file mode 100644 index 3b6dcc5cb..000000000 --- a/projects/diagnostic_procedure/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [diag:extractionResult__input_text](http://w3id.org/ontogpt/diagnostic_procedure/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/diagnostic_procedure/docs/extractionResult__input_title.md b/projects/diagnostic_procedure/docs/extractionResult__input_title.md deleted file mode 100644 index e37e7429b..000000000 --- a/projects/diagnostic_procedure/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [diag:extractionResult__input_title](http://w3id.org/ontogpt/diagnostic_procedure/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/diagnostic_procedure/docs/extractionResult__named_entities.md b/projects/diagnostic_procedure/docs/extractionResult__named_entities.md deleted file mode 100644 index 2246afb9c..000000000 --- a/projects/diagnostic_procedure/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [diag:extractionResult__named_entities](http://w3id.org/ontogpt/diagnostic_procedure/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/diagnostic_procedure/docs/extractionResult__prompt.md b/projects/diagnostic_procedure/docs/extractionResult__prompt.md deleted file mode 100644 index 20fdaaccf..000000000 --- a/projects/diagnostic_procedure/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [diag:extractionResult__prompt](http://w3id.org/ontogpt/diagnostic_procedure/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/diagnostic_procedure/docs/extractionResult__raw_completion_output.md b/projects/diagnostic_procedure/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 554805c0f..000000000 --- a/projects/diagnostic_procedure/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [diag:extractionResult__raw_completion_output](http://w3id.org/ontogpt/diagnostic_procedure/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/diagnostic_procedure/docs/namedEntity__id.md b/projects/diagnostic_procedure/docs/namedEntity__id.md deleted file mode 100644 index 7413eb383..000000000 --- a/projects/diagnostic_procedure/docs/namedEntity__id.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [diag:namedEntity__id](http://w3id.org/ontogpt/diagnostic_procedure/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ClinicalAttribute](ClinicalAttribute.md) - * [DiagnosticProcedure](DiagnosticProcedure.md) - * [NamedEntity](NamedEntity.md) - * [Phenotype](Phenotype.md) - * [ProcedureToAttributePredicate](ProcedureToAttributePredicate.md) - * [ProcedureToPhenotypePredicate](ProcedureToPhenotypePredicate.md) - * [Quality](Quality.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/diagnostic_procedure/docs/namedEntity__label.md b/projects/diagnostic_procedure/docs/namedEntity__label.md deleted file mode 100644 index 2c32cb0e8..000000000 --- a/projects/diagnostic_procedure/docs/namedEntity__label.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [diag:namedEntity__label](http://w3id.org/ontogpt/diagnostic_procedure/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ClinicalAttribute](ClinicalAttribute.md) - * [DiagnosticProcedure](DiagnosticProcedure.md) - * [NamedEntity](NamedEntity.md) - * [Phenotype](Phenotype.md) - * [ProcedureToAttributePredicate](ProcedureToAttributePredicate.md) - * [ProcedureToPhenotypePredicate](ProcedureToPhenotypePredicate.md) - * [Quality](Quality.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/diagnostic_procedure/docs/publication__abstract.md b/projects/diagnostic_procedure/docs/publication__abstract.md deleted file mode 100644 index a23d8005d..000000000 --- a/projects/diagnostic_procedure/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [diag:publication__abstract](http://w3id.org/ontogpt/diagnostic_procedure/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/diagnostic_procedure/docs/publication__combined_text.md b/projects/diagnostic_procedure/docs/publication__combined_text.md deleted file mode 100644 index 8d5296d47..000000000 --- a/projects/diagnostic_procedure/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [diag:publication__combined_text](http://w3id.org/ontogpt/diagnostic_procedure/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/diagnostic_procedure/docs/publication__full_text.md b/projects/diagnostic_procedure/docs/publication__full_text.md deleted file mode 100644 index 770358251..000000000 --- a/projects/diagnostic_procedure/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [diag:publication__full_text](http://w3id.org/ontogpt/diagnostic_procedure/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/diagnostic_procedure/docs/publication__id.md b/projects/diagnostic_procedure/docs/publication__id.md deleted file mode 100644 index b301de365..000000000 --- a/projects/diagnostic_procedure/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [diag:publication__id](http://w3id.org/ontogpt/diagnostic_procedure/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/diagnostic_procedure/docs/publication__title.md b/projects/diagnostic_procedure/docs/publication__title.md deleted file mode 100644 index a29167a8e..000000000 --- a/projects/diagnostic_procedure/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [diag:publication__title](http://w3id.org/ontogpt/diagnostic_procedure/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/diagnostic_procedure/docs/textWithTriples__publication.md b/projects/diagnostic_procedure/docs/textWithTriples__publication.md deleted file mode 100644 index 69860f0a5..000000000 --- a/projects/diagnostic_procedure/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [diag:textWithTriples__publication](http://w3id.org/ontogpt/diagnostic_procedure/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/diagnostic_procedure/docs/textWithTriples__triples.md b/projects/diagnostic_procedure/docs/textWithTriples__triples.md deleted file mode 100644 index 7da8f2bbc..000000000 --- a/projects/diagnostic_procedure/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [diag:textWithTriples__triples](http://w3id.org/ontogpt/diagnostic_procedure/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/diagnostic_procedure/docs/triple__object.md b/projects/diagnostic_procedure/docs/triple__object.md deleted file mode 100644 index 9867ef445..000000000 --- a/projects/diagnostic_procedure/docs/triple__object.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: object - - - - -URI: [diag:triple__object](http://w3id.org/ontogpt/diagnostic_procedure/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [DiagnosticProceduretoAttributeAssociation➞object](DiagnosticProceduretoAttributeAssociation_object.md) - * [DiagnosticProceduretoPhenotypeAssociation➞object](DiagnosticProceduretoPhenotypeAssociation_object.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/diagnostic_procedure/docs/triple__object_qualifier.md b/projects/diagnostic_procedure/docs/triple__object_qualifier.md deleted file mode 100644 index 4bd449f17..000000000 --- a/projects/diagnostic_procedure/docs/triple__object_qualifier.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [diag:triple__object_qualifier](http://w3id.org/ontogpt/diagnostic_procedure/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [DiagnosticProceduretoAttributeAssociation➞object_qualifier](DiagnosticProceduretoAttributeAssociation_object_qualifier.md) - * [DiagnosticProceduretoPhenotypeAssociation➞object_qualifier](DiagnosticProceduretoPhenotypeAssociation_object_qualifier.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/diagnostic_procedure/docs/triple__predicate.md b/projects/diagnostic_procedure/docs/triple__predicate.md deleted file mode 100644 index 79146dc19..000000000 --- a/projects/diagnostic_procedure/docs/triple__predicate.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: predicate - - - - -URI: [diag:triple__predicate](http://w3id.org/ontogpt/diagnostic_procedure/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - * [DiagnosticProceduretoAttributeAssociation➞predicate](DiagnosticProceduretoAttributeAssociation_predicate.md) - * [DiagnosticProceduretoPhenotypeAssociation➞predicate](DiagnosticProceduretoPhenotypeAssociation_predicate.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/diagnostic_procedure/docs/triple__qualifier.md b/projects/diagnostic_procedure/docs/triple__qualifier.md deleted file mode 100644 index baeed3656..000000000 --- a/projects/diagnostic_procedure/docs/triple__qualifier.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [diag:triple__qualifier](http://w3id.org/ontogpt/diagnostic_procedure/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [DiagnosticProceduretoAttributeAssociation](DiagnosticProceduretoAttributeAssociation.md) - * [DiagnosticProceduretoPhenotypeAssociation](DiagnosticProceduretoPhenotypeAssociation.md) - * [Triple](Triple.md) diff --git a/projects/diagnostic_procedure/docs/triple__subject.md b/projects/diagnostic_procedure/docs/triple__subject.md deleted file mode 100644 index ef43fd56e..000000000 --- a/projects/diagnostic_procedure/docs/triple__subject.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: subject - - - - -URI: [diag:triple__subject](http://w3id.org/ontogpt/diagnostic_procedure/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [DiagnosticProceduretoAttributeAssociation➞subject](DiagnosticProceduretoAttributeAssociation_subject.md) - * [DiagnosticProceduretoPhenotypeAssociation➞subject](DiagnosticProceduretoPhenotypeAssociation_subject.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/diagnostic_procedure/docs/triple__subject_qualifier.md b/projects/diagnostic_procedure/docs/triple__subject_qualifier.md deleted file mode 100644 index c0f1c2604..000000000 --- a/projects/diagnostic_procedure/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [diag:triple__subject_qualifier](http://w3id.org/ontogpt/diagnostic_procedure/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [DiagnosticProceduretoAttributeAssociation➞subject_qualifier](DiagnosticProceduretoAttributeAssociation_subject_qualifier.md) - * [DiagnosticProceduretoPhenotypeAssociation➞subject_qualifier](DiagnosticProceduretoPhenotypeAssociation_subject_qualifier.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/diagnostic_procedure/docs/types/Boolean.md b/projects/diagnostic_procedure/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/diagnostic_procedure/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/diagnostic_procedure/docs/types/Curie.md b/projects/diagnostic_procedure/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/diagnostic_procedure/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/diagnostic_procedure/docs/types/Date.md b/projects/diagnostic_procedure/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/diagnostic_procedure/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/diagnostic_procedure/docs/types/DateOrDatetime.md b/projects/diagnostic_procedure/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/diagnostic_procedure/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/diagnostic_procedure/docs/types/Datetime.md b/projects/diagnostic_procedure/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/diagnostic_procedure/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/diagnostic_procedure/docs/types/Decimal.md b/projects/diagnostic_procedure/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/diagnostic_procedure/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/diagnostic_procedure/docs/types/Double.md b/projects/diagnostic_procedure/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/diagnostic_procedure/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/diagnostic_procedure/docs/types/Float.md b/projects/diagnostic_procedure/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/diagnostic_procedure/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/diagnostic_procedure/docs/types/Integer.md b/projects/diagnostic_procedure/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/diagnostic_procedure/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/diagnostic_procedure/docs/types/Jsonpath.md b/projects/diagnostic_procedure/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/diagnostic_procedure/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/diagnostic_procedure/docs/types/Jsonpointer.md b/projects/diagnostic_procedure/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/diagnostic_procedure/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/diagnostic_procedure/docs/types/Ncname.md b/projects/diagnostic_procedure/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/diagnostic_procedure/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/diagnostic_procedure/docs/types/Nodeidentifier.md b/projects/diagnostic_procedure/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/diagnostic_procedure/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/diagnostic_procedure/docs/types/Objectidentifier.md b/projects/diagnostic_procedure/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/diagnostic_procedure/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/diagnostic_procedure/docs/types/Sparqlpath.md b/projects/diagnostic_procedure/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/diagnostic_procedure/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/diagnostic_procedure/docs/types/String.md b/projects/diagnostic_procedure/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/diagnostic_procedure/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/diagnostic_procedure/docs/types/Time.md b/projects/diagnostic_procedure/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/diagnostic_procedure/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/diagnostic_procedure/docs/types/Uri.md b/projects/diagnostic_procedure/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/diagnostic_procedure/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with 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ze{)aF|IhHfn~MDF^7i2Ym9^i&{5F0cO8lQN)%d@M`E39{RHHv(6bXM1^V<l1D5d@l z13pJ|5A#!4J*4$vC;Zd&<&$6f;)jM0JIkMjf~5am`oH?jhsF=PiJ!*7<oCvZ=q(=N jJglrgak?meTW1wyph4$v!N71pKe(W8;-HhbU||0T?7+HA diff --git a/projects/diagnostic_procedure/graphql/diagnostic_procedure.graphql b/projects/diagnostic_procedure/graphql/diagnostic_procedure.graphql deleted file mode 100644 index 152e88aac..000000000 --- a/projects/diagnostic_procedure/graphql/diagnostic_procedure.graphql +++ /dev/null @@ -1,126 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type ClinicalAttribute - { - id: String! - label: String - unit: Unit - } - -interface CompoundExpression - { - } - -type DiagnosticProcedure - { - id: String! - label: String - } - -type DiagnosticProceduretoAttributeAssociation - { - qualifier: String - subject: DiagnosticProcedure - object: [ClinicalAttribute] - predicate: ProcedureToAttributePredicate - subjectQualifier: NamedEntity - objectQualifier: Quality - } - -type DiagnosticProceduretoPhenotypeAssociation - { - qualifier: String - subject: DiagnosticProcedure - object: [Phenotype] - predicate: ProcedureToPhenotypePredicate - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -interface NamedEntity - { - id: String! - label: String - } - -type Phenotype - { - id: String! - label: String - } - -type ProcedureToAttributePredicate - { - id: String! - label: String - } - -type ProcedureToPhenotypePredicate - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type Quality - { - id: String! - label: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - -type Unit - { - id: String! - label: String - } - diff --git a/projects/diagnostic_procedure/jsonld/diagnostic_procedure.context.jsonld b/projects/diagnostic_procedure/jsonld/diagnostic_procedure.context.jsonld deleted file mode 100644 index d5d39d283..000000000 --- a/projects/diagnostic_procedure/jsonld/diagnostic_procedure.context.jsonld +++ /dev/null @@ -1,144 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:52:28", - "source": "diagnostic_procedure.yaml" - }, - "@context": { - "HP": { - "@id": "http://purl.obolibrary.org/obo/HP_", - "@prefix": true - }, - "LOINC": "http://loinc.org/rdf/", - "OBA": { - "@id": "http://purl.obolibrary.org/obo/OBA_", - "@prefix": true - }, - "PATO": { - "@id": "http://purl.obolibrary.org/obo/PATO_", - "@prefix": true - }, - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "UO": "http://example.org/UNKNOWN/UO/", - "biolink": "https://w3id.org/biolink/vocab/", - "core": "http://w3id.org/ontogpt/core/", - "diag": "http://w3id.org/ontogpt/diagnostic_procedure/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/diagnostic_procedure/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "unit": { - "@type": "@id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/diagnostic_procedure/jsonld/diagnostic_procedure.jsonld b/projects/diagnostic_procedure/jsonld/diagnostic_procedure.jsonld deleted file mode 100644 index 93b7cfd9e..000000000 --- a/projects/diagnostic_procedure/jsonld/diagnostic_procedure.jsonld +++ /dev/null @@ -1,1368 +0,0 @@ -{ - "name": "diagnostic_procedure", - "description": "A template for clinical diagnostic procedures and the phenotypes they may contribute to.", - "title": "Diagnostic Procedure Template", - "id": "http://w3id.org/ontogpt/diagnostic_procedure", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "diag", - "prefix_reference": "http://w3id.org/ontogpt/diagnostic_procedure/" - }, - { - "prefix_prefix": "LOINC", - "prefix_reference": "http://loinc.org/rdf/" - }, - { - "prefix_prefix": "HP", - "prefix_reference": "http://purl.obolibrary.org/obo/HP_" - }, - { - "prefix_prefix": "RO", - "prefix_reference": "http://purl.obolibrary.org/obo/RO_" - }, - { - "prefix_prefix": "OBA", - "prefix_reference": "http://purl.obolibrary.org/obo/OBA_" - }, - { - "prefix_prefix": "PATO", - "prefix_reference": "http://purl.obolibrary.org/obo/PATO_" - }, - { - "prefix_prefix": "biolink", - "prefix_reference": "https://w3id.org/biolink/vocab/" - } - ], - "default_prefix": "diag", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "clinicalAttribute__unit", - "description": "the unit used to measure the attribute", - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "slot_uri": "http://w3id.org/ontogpt/diagnostic_procedure/unit", - "alias": "unit", - "owner": "ClinicalAttribute", - "domain_of": [ - "ClinicalAttribute" - ], - "range": "Unit", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "DiagnosticProceduretoPhenotypeAssociation_subject", - "description": "A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit.", - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "triple__subject", - "domain": "DiagnosticProceduretoPhenotypeAssociation", - "slot_uri": "http://w3id.org/ontogpt/diagnostic_procedure/subject", - "alias": "subject", - "owner": "DiagnosticProceduretoPhenotypeAssociation", - "domain_of": [ - "DiagnosticProceduretoPhenotypeAssociation" - ], - "is_usage_slot": true, - "usage_slot_name": "subject", - "range": "DiagnosticProcedure", - "@type": "SlotDefinition" - }, - { - "name": "DiagnosticProceduretoPhenotypeAssociation_object", - "description": "The observable physical or biochemical characteristics of a patient. Not equivalent to a disease state, but may contribute to a diagnosis.", - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "triple__object", - "domain": "DiagnosticProceduretoPhenotypeAssociation", - "slot_uri": "http://w3id.org/ontogpt/diagnostic_procedure/object", - "multivalued": true, - "alias": "object", - "owner": "DiagnosticProceduretoPhenotypeAssociation", - "domain_of": [ - "DiagnosticProceduretoPhenotypeAssociation" - ], - "is_usage_slot": true, - "usage_slot_name": "object", - "range": "Phenotype", - "@type": "SlotDefinition" - }, - { - "name": "DiagnosticProceduretoPhenotypeAssociation_predicate", - "description": "The relationship type, e.g. RELATED_TO", - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "triple__predicate", - "domain": "DiagnosticProceduretoPhenotypeAssociation", - "slot_uri": "http://w3id.org/ontogpt/diagnostic_procedure/predicate", - "alias": "predicate", - "owner": "DiagnosticProceduretoPhenotypeAssociation", - "domain_of": [ - "DiagnosticProceduretoPhenotypeAssociation" - ], - "is_usage_slot": true, - "usage_slot_name": "predicate", - "range": "ProcedureToPhenotypePredicate", - "@type": "SlotDefinition" - }, - { - "name": "DiagnosticProceduretoPhenotypeAssociation_subject_qualifier", - "description": "An optional qualifier or modifier for the procedure.", - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "triple__subject_qualifier", - "domain": "DiagnosticProceduretoPhenotypeAssociation", - "slot_uri": "http://w3id.org/ontogpt/diagnostic_procedure/subject_qualifier", - "alias": "subject_qualifier", - "owner": "DiagnosticProceduretoPhenotypeAssociation", - "domain_of": [ - "DiagnosticProceduretoPhenotypeAssociation" - ], - "is_usage_slot": true, - "usage_slot_name": "subject_qualifier", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "DiagnosticProceduretoPhenotypeAssociation_object_qualifier", - "description": "An optional qualifier or modifier for the phenotype.", - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "triple__object_qualifier", - "domain": "DiagnosticProceduretoPhenotypeAssociation", - "slot_uri": "http://w3id.org/ontogpt/diagnostic_procedure/object_qualifier", - "alias": "object_qualifier", - "owner": "DiagnosticProceduretoPhenotypeAssociation", - "domain_of": [ - "DiagnosticProceduretoPhenotypeAssociation" - ], - "is_usage_slot": true, - "usage_slot_name": "object_qualifier", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "DiagnosticProceduretoAttributeAssociation_subject", - "description": "A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit.", - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "triple__subject", - "domain": "DiagnosticProceduretoAttributeAssociation", - "slot_uri": "http://w3id.org/ontogpt/diagnostic_procedure/subject", - "alias": "subject", - "owner": "DiagnosticProceduretoAttributeAssociation", - "domain_of": [ - "DiagnosticProceduretoAttributeAssociation" - ], - "is_usage_slot": true, - "usage_slot_name": "subject", - "range": "DiagnosticProcedure", - "@type": "SlotDefinition" - }, - { - "name": "DiagnosticProceduretoAttributeAssociation_object", - "description": "Any measurable clinical attribute.", - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "triple__object", - "domain": "DiagnosticProceduretoAttributeAssociation", - "slot_uri": "http://w3id.org/ontogpt/diagnostic_procedure/object", - "multivalued": true, - "alias": "object", - "owner": "DiagnosticProceduretoAttributeAssociation", - "domain_of": [ - "DiagnosticProceduretoAttributeAssociation" - ], - "is_usage_slot": true, - "usage_slot_name": "object", - "range": "ClinicalAttribute", - "@type": "SlotDefinition" - }, - { - "name": "DiagnosticProceduretoAttributeAssociation_predicate", - "description": "The relationship type, e.g. RELATED_TO", - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "triple__predicate", - "domain": "DiagnosticProceduretoAttributeAssociation", - "slot_uri": "http://w3id.org/ontogpt/diagnostic_procedure/predicate", - "alias": "predicate", - "owner": "DiagnosticProceduretoAttributeAssociation", - "domain_of": [ - "DiagnosticProceduretoAttributeAssociation" - ], - "is_usage_slot": true, - "usage_slot_name": "predicate", - "range": "ProcedureToAttributePredicate", - "@type": "SlotDefinition" - }, - { - "name": "DiagnosticProceduretoAttributeAssociation_subject_qualifier", - "description": "An optional qualifier or modifier for the procedure.", - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "triple__subject_qualifier", - "domain": "DiagnosticProceduretoAttributeAssociation", - "slot_uri": "http://w3id.org/ontogpt/diagnostic_procedure/subject_qualifier", - "alias": "subject_qualifier", - "owner": "DiagnosticProceduretoAttributeAssociation", - "domain_of": [ - "DiagnosticProceduretoAttributeAssociation" - ], - "is_usage_slot": true, - "usage_slot_name": "subject_qualifier", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "DiagnosticProceduretoAttributeAssociation_object_qualifier", - "description": "An optional qualifier or modifier for the phenotype.", - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "triple__object_qualifier", - "domain": "DiagnosticProceduretoAttributeAssociation", - "slot_uri": "http://w3id.org/ontogpt/diagnostic_procedure/object_qualifier", - "alias": "object_qualifier", - "owner": "DiagnosticProceduretoAttributeAssociation", - "domain_of": [ - "DiagnosticProceduretoAttributeAssociation" - ], - "is_usage_slot": true, - "usage_slot_name": "object_qualifier", - "range": "Quality", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "DiagnosticProceduretoPhenotypeAssociation", - "definition_uri": "http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation", - "description": "A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high blood pressure\".", - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "Triple", - "slots": [ - "triple__qualifier", - "DiagnosticProceduretoPhenotypeAssociation_subject", - "DiagnosticProceduretoPhenotypeAssociation_object", - "DiagnosticProceduretoPhenotypeAssociation_predicate", - "DiagnosticProceduretoPhenotypeAssociation_subject_qualifier", - "DiagnosticProceduretoPhenotypeAssociation_object_qualifier" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation", - "@type": "ClassDefinition" - }, - { - "name": "DiagnosticProceduretoAttributeAssociation", - "definition_uri": "http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoAttributeAssociation", - "description": "A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\").", - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "Triple", - "slots": [ - "triple__qualifier", - "DiagnosticProceduretoAttributeAssociation_subject", - "DiagnosticProceduretoAttributeAssociation_object", - "DiagnosticProceduretoAttributeAssociation_predicate", - "DiagnosticProceduretoAttributeAssociation_subject_qualifier", - "DiagnosticProceduretoAttributeAssociation_object_qualifier" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoAttributeAssociation", - "@type": "ClassDefinition" - }, - { - "name": "DiagnosticProcedure", - "id_prefixes": [ - "LOINC" - ], - "definition_uri": "http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProcedure", - "annotations": [ - { - "tag": "annotators", - "value": "bioportal:loinc, sqlite:obo:ncit", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProcedure", - "@type": "ClassDefinition" - }, - { - "name": "Phenotype", - "id_prefixes": [ - "HP" - ], - "definition_uri": "http://w3id.org/ontogpt/diagnostic_procedure/Phenotype", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:hp", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/diagnostic_procedure/Phenotype", - "@type": "ClassDefinition" - }, - { - "name": "ClinicalAttribute", - "id_prefixes": [ - "OBA" - ], - "definition_uri": "http://w3id.org/ontogpt/diagnostic_procedure/ClinicalAttribute", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:oba, sqlite:obo:ncit", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label", - "clinicalAttribute__unit" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "unit", - "description": "the unit used to measure the attribute", - "range": "Unit", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/diagnostic_procedure/ClinicalAttribute", - "@type": "ClassDefinition" - }, - { - "name": "Quality", - "id_prefixes": [ - "PATO" - ], - "definition_uri": "http://w3id.org/ontogpt/diagnostic_procedure/Quality", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:pato", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/diagnostic_procedure/Quality", - "@type": "ClassDefinition" - }, - { - "name": "ProcedureToPhenotypePredicate", - "definition_uri": "http://w3id.org/ontogpt/diagnostic_procedure/ProcedureToPhenotypePredicate", - "description": "A predicate for procedure to phenotype relationships, defining \"this procedure is intended to provide support for/against this phenotype\".", - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "RelationshipType", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/diagnostic_procedure/ProcedureToPhenotypePredicate", - "@type": "ClassDefinition" - }, - { - "name": "ProcedureToAttributePredicate", - "definition_uri": "http://w3id.org/ontogpt/diagnostic_procedure/ProcedureToAttributePredicate", - "description": "A predicate for procedure to attribute relationships, defining \"this procedure is a measurement of this attribute\".", - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "RelationshipType", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/diagnostic_procedure/ProcedureToAttributePredicate", - "@type": "ClassDefinition" - }, - { - "name": "Unit", - "id_prefixes": [ - "UO" - ], - "definition_uri": "http://w3id.org/ontogpt/diagnostic_procedure/Unit", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:uo", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/diagnostic_procedure", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/diagnostic_procedure/Unit", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "diagnostic_procedure.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 4774, - "generation_date": "2023-08-07T10:52:29", - "@type": "SchemaDefinition", - "@context": [ - "projects/diagnostic_procedure/jsonld/diagnostic_procedure.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/diagnostic_procedure/" - } - ] -} diff --git a/projects/diagnostic_procedure/jsonschema/diagnostic_procedure.schema.json b/projects/diagnostic_procedure/jsonschema/diagnostic_procedure.schema.json deleted file mode 100644 index d573d848c..000000000 --- a/projects/diagnostic_procedure/jsonschema/diagnostic_procedure.schema.json +++ /dev/null @@ -1,348 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ClinicalAttribute": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - }, - "unit": { - "description": "the unit used to measure the attribute", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ClinicalAttribute", - "type": "object" - }, - "DiagnosticProcedure": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "DiagnosticProcedure", - "type": "object" - }, - "DiagnosticProceduretoAttributeAssociation": { - "additionalProperties": false, - "description": "A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\").", - "properties": { - "object": { - "description": "Any measurable clinical attribute.", - "items": { - "type": "string" - }, - "type": "array" - }, - "object_qualifier": { - "description": "An optional qualifier or modifier for the phenotype.", - "type": "string" - }, - "predicate": { - "description": "The relationship type, e.g. RELATED_TO", - "type": "string" - }, - "qualifier": { - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "type": "string" - }, - "subject": { - "description": "A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit.", - "type": "string" - }, - "subject_qualifier": { - "description": "An optional qualifier or modifier for the procedure.", - "type": "string" - } - }, - "title": "DiagnosticProceduretoAttributeAssociation", - "type": "object" - }, - "DiagnosticProceduretoPhenotypeAssociation": { - "additionalProperties": false, - "description": "A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high blood pressure\".", - "properties": { - "object": { - "description": "The observable physical or biochemical characteristics of a patient. Not equivalent to a disease state, but may contribute to a diagnosis.", - "items": { - "type": "string" - }, - "type": "array" - }, - "object_qualifier": { - "description": "An optional qualifier or modifier for the phenotype.", - "type": "string" - }, - "predicate": { - "description": "The relationship type, e.g. RELATED_TO", - "type": "string" - }, - "qualifier": { - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "type": "string" - }, - "subject": { - "description": "A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit.", - "type": "string" - }, - "subject_qualifier": { - "description": "An optional qualifier or modifier for the procedure.", - "type": "string" - } - }, - "title": "DiagnosticProceduretoPhenotypeAssociation", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Phenotype": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Phenotype", - "type": "object" - }, - "ProcedureToAttributePredicate": { - "additionalProperties": false, - "description": "A predicate for procedure to attribute relationships, defining \"this procedure is a measurement of this attribute\".", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ProcedureToAttributePredicate", - "type": "object" - }, - "ProcedureToPhenotypePredicate": { - "additionalProperties": false, - "description": "A predicate for procedure to phenotype relationships, defining \"this procedure is intended to provide support for/against this phenotype\".", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ProcedureToPhenotypePredicate", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "Quality": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Quality", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Unit": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Unit", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/diagnostic_procedure", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "diagnostic_procedure", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/diagnostic_procedure/owl/diagnostic_procedure.owl.ttl b/projects/diagnostic_procedure/owl/diagnostic_procedure.owl.ttl deleted file mode 100644 index 9b827e802..000000000 --- a/projects/diagnostic_procedure/owl/diagnostic_procedure.owl.ttl +++ /dev/null @@ -1,527 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix diag: <http://w3id.org/ontogpt/diagnostic_procedure/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/diagnostic_procedure> a owl:Ontology ; - rdfs:label "diagnostic_procedure" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples> ; - linkml:classes "{'DiagnosticProceduretoPhenotypeAssociation': ClassDefinition(name='DiagnosticProceduretoPhenotypeAssociation', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoPhenotypeAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high blood pressure\".', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='Triple', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__qualifier', 'DiagnosticProceduretoPhenotypeAssociation_subject', 'DiagnosticProceduretoPhenotypeAssociation_object', 'DiagnosticProceduretoPhenotypeAssociation_predicate', 'DiagnosticProceduretoPhenotypeAssociation_subject_qualifier', 'DiagnosticProceduretoPhenotypeAssociation_object_qualifier'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DiagnosticProcedure', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The observable physical or biochemical characteristics of a patient. Not equivalent to a disease state, but may contribute to a diagnosis.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Phenotype', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The relationship type, e.g. RELATED_TO', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__predicate', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ProcedureToPhenotypePredicate', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the procedure.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the phenotype.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='diag:DiagnosticProceduretoPhenotypeAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'DiagnosticProceduretoAttributeAssociation': ClassDefinition(name='DiagnosticProceduretoAttributeAssociation', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProceduretoAttributeAssociation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\").', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='Triple', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__qualifier', 'DiagnosticProceduretoAttributeAssociation_subject', 'DiagnosticProceduretoAttributeAssociation_object', 'DiagnosticProceduretoAttributeAssociation_predicate', 'DiagnosticProceduretoAttributeAssociation_subject_qualifier', 'DiagnosticProceduretoAttributeAssociation_object_qualifier'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DiagnosticProcedure', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Any measurable clinical attribute.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ClinicalAttribute', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The relationship type, e.g. RELATED_TO', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__predicate', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ProcedureToAttributePredicate', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the procedure.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the phenotype.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Quality', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='diag:DiagnosticProceduretoAttributeAssociation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'DiagnosticProcedure': ClassDefinition(name='DiagnosticProcedure', id_prefixes=['LOINC'], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/DiagnosticProcedure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='bioportal:loinc, sqlite:obo:ncit', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='diag:DiagnosticProcedure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Phenotype': ClassDefinition(name='Phenotype', id_prefixes=['HP'], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/Phenotype', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hp', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='diag:Phenotype', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ClinicalAttribute': ClassDefinition(name='ClinicalAttribute', id_prefixes=['OBA'], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/ClinicalAttribute', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:oba, sqlite:obo:ncit', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label', 'clinicalAttribute__unit'], slot_usage={}, attributes={'unit': SlotDefinition(name='unit', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the unit used to measure the attribute', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Unit', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='diag:ClinicalAttribute', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Quality': ClassDefinition(name='Quality', id_prefixes=['PATO'], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/Quality', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:pato', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='diag:Quality', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ProcedureToPhenotypePredicate': ClassDefinition(name='ProcedureToPhenotypePredicate', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/ProcedureToPhenotypePredicate', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A predicate for procedure to phenotype relationships, defining \"this procedure is intended to provide support for/against this phenotype\".', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='RelationshipType', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='diag:ProcedureToPhenotypePredicate', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ProcedureToAttributePredicate': ClassDefinition(name='ProcedureToAttributePredicate', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/ProcedureToAttributePredicate', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A predicate for procedure to attribute relationships, defining \"this procedure is a measurement of this attribute\".', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='RelationshipType', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='diag:ProcedureToAttributePredicate', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Unit': ClassDefinition(name='Unit', id_prefixes=['UO'], definition_uri='http://w3id.org/ontogpt/diagnostic_procedure/Unit', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:uo', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/diagnostic_procedure', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='diag:Unit', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/diagnostic_procedure" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - diag:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -diag:unit a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "unit" ; - rdfs:range diag:Unit ; - skos:definition "the unit used to measure the attribute" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - diag:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -diag:ClinicalAttribute a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ClinicalAttribute" ; - diag:annotators "sqlite:obo:oba, sqlite:obo:ncit" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass diag:Unit ; - owl:onProperty diag:unit ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{'unit': SlotDefinition(name='unit', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the unit used to measure the attribute', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Unit', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - -diag:Phenotype a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Phenotype" ; - diag:annotators "sqlite:obo:hp" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -diag:ProcedureToAttributePredicate a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ProcedureToAttributePredicate" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/RelationshipType> ; - skos:definition "A predicate for procedure to attribute relationships, defining \"this procedure is a measurement of this attribute\"." ; - linkml:attributes "{}" ; - linkml:is_a "RelationshipType" . - -diag:ProcedureToPhenotypePredicate a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ProcedureToPhenotypePredicate" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/RelationshipType> ; - skos:definition "A predicate for procedure to phenotype relationships, defining \"this procedure is intended to provide support for/against this phenotype\"." ; - linkml:attributes "{}" ; - linkml:is_a "RelationshipType" . - -diag:Quality a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Quality" ; - diag:annotators "sqlite:obo:pato" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -diag:Unit a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Unit" ; - diag:annotators "sqlite:obo:uo" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -diag:object a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:domain diag:DiagnosticProceduretoAttributeAssociation, - diag:DiagnosticProceduretoPhenotypeAssociation ; - rdfs:range diag:ClinicalAttribute, - diag:Phenotype ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/object> ; - skos:definition "Any measurable clinical attribute.", - "The observable physical or biochemical characteristics of a patient. Not equivalent to a disease state, but may contribute to a diagnosis." ; - linkml:is_a "triple__object" . - -diag:object_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:domain diag:DiagnosticProceduretoAttributeAssociation, - diag:DiagnosticProceduretoPhenotypeAssociation ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity>, - diag:Quality ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/object_qualifier> ; - skos:definition "An optional qualifier or modifier for the phenotype." ; - linkml:is_a "triple__object_qualifier" . - -diag:predicate a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:domain diag:DiagnosticProceduretoAttributeAssociation, - diag:DiagnosticProceduretoPhenotypeAssociation ; - rdfs:range diag:ProcedureToAttributePredicate, - diag:ProcedureToPhenotypePredicate ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/predicate> ; - skos:definition "The relationship type, e.g. RELATED_TO" ; - linkml:is_a "triple__predicate" . - -diag:subject a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:domain diag:DiagnosticProceduretoAttributeAssociation, - diag:DiagnosticProceduretoPhenotypeAssociation ; - rdfs:range diag:DiagnosticProcedure ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/subject> ; - skos:definition "A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit." ; - linkml:is_a "triple__subject" . - -diag:subject_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:domain diag:DiagnosticProceduretoAttributeAssociation, - diag:DiagnosticProceduretoPhenotypeAssociation ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/subject_qualifier> ; - skos:definition "An optional qualifier or modifier for the procedure." ; - linkml:is_a "triple__subject_qualifier" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -diag:DiagnosticProcedure a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DiagnosticProcedure" ; - diag:annotators "bioportal:loinc, sqlite:obo:ncit" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -diag:DiagnosticProceduretoAttributeAssociation a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DiagnosticProceduretoAttributeAssociation" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass diag:Quality ; - owl:onProperty diag:object_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass diag:ProcedureToAttributePredicate ; - owl:onProperty diag:predicate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass diag:DiagnosticProcedure ; - owl:onProperty diag:subject ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty diag:subject_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom diag:ClinicalAttribute ; - owl:onProperty diag:object ], - <http://w3id.org/ontogpt/core/Triple> ; - skos:definition "A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\")." ; - linkml:attributes "{}" ; - linkml:is_a "Triple" . - -diag:DiagnosticProceduretoPhenotypeAssociation a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DiagnosticProceduretoPhenotypeAssociation" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass diag:ProcedureToPhenotypePredicate ; - owl:onProperty diag:predicate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty diag:subject_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty diag:object_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom diag:Phenotype ; - owl:onProperty diag:object ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass diag:DiagnosticProcedure ; - owl:onProperty diag:subject ], - <http://w3id.org/ontogpt/core/Triple> ; - skos:definition "A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high blood pressure\"." ; - linkml:attributes "{}" ; - linkml:is_a "Triple" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/diagnostic_procedure/prefixmap/diagnostic_procedure.yaml b/projects/diagnostic_procedure/prefixmap/diagnostic_procedure.yaml deleted file mode 100644 index 5f652360b..000000000 --- a/projects/diagnostic_procedure/prefixmap/diagnostic_procedure.yaml +++ /dev/null @@ -1,40 +0,0 @@ -{ - "HP": "http://purl.obolibrary.org/obo/HP_", - "LOINC": "http://loinc.org/rdf/", - "OBA": "http://purl.obolibrary.org/obo/OBA_", - "PATO": "http://purl.obolibrary.org/obo/PATO_", - "RO": "http://purl.obolibrary.org/obo/RO_", - "UO": "http://example.org/UNKNOWN/UO/", - "biolink": "https://w3id.org/biolink/vocab/", - "core": "http://w3id.org/ontogpt/core/", - "diag": "http://w3id.org/ontogpt/diagnostic_procedure/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/diagnostic_procedure/protobuf/diagnostic_procedure.proto b/projects/diagnostic_procedure/protobuf/diagnostic_procedure.proto deleted file mode 100644 index d888ad452..000000000 --- a/projects/diagnostic_procedure/protobuf/diagnostic_procedure.proto +++ /dev/null @@ -1,93 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message ClinicalAttribute - { - string id = 0 - string label = 0 - unit unit = 0 - } -message DiagnosticProcedure - { - string id = 0 - string label = 0 - } -// A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., "blood pressure measurement" is associated with "blood pressure" (or in OBA, something like OBA:VT0000183, "blood pressure trait"). -message DiagnosticProceduretoAttributeAssociation - { - string qualifier = 0 - diagnosticProcedure subject = 0 - repeated clinicalAttribute object = 0 - procedureToAttributePredicate predicate = 0 - namedEntity subjectQualifier = 0 - quality objectQualifier = 0 - } -// A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., "blood pressure measurement" is associated with "high blood pressure". -message DiagnosticProceduretoPhenotypeAssociation - { - string qualifier = 0 - diagnosticProcedure subject = 0 - repeated phenotype object = 0 - procedureToPhenotypePredicate predicate = 0 - namedEntity subjectQualifier = 0 - namedEntity objectQualifier = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Phenotype - { - string id = 0 - string label = 0 - } -// A predicate for procedure to attribute relationships, defining "this procedure is a measurement of this attribute". -message ProcedureToAttributePredicate - { - string id = 0 - string label = 0 - } -// A predicate for procedure to phenotype relationships, defining "this procedure is intended to provide support for/against this phenotype". -message ProcedureToPhenotypePredicate - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message Quality - { - string id = 0 - string label = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Unit - { - string id = 0 - string label = 0 - } diff --git a/projects/diagnostic_procedure/shacl/diagnostic_procedure.shacl.ttl b/projects/diagnostic_procedure/shacl/diagnostic_procedure.shacl.ttl deleted file mode 100644 index 811707381..000000000 --- a/projects/diagnostic_procedure/shacl/diagnostic_procedure.shacl.ttl +++ /dev/null @@ -1,348 +0,0 @@ -@prefix diag: <http://w3id.org/ontogpt/diagnostic_procedure/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -diag:DiagnosticProceduretoAttributeAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A triple representing a relationship between a diagnostic procedure and a measured attribute, e.g., \"blood pressure measurement\" is associated with \"blood pressure\" (or in OBA, something like OBA:VT0000183, \"blood pressure trait\")." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class diag:ProcedureToAttributePredicate ; - sh:description "The relationship type, e.g. RELATED_TO" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class diag:DiagnosticProcedure ; - sh:description "A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class diag:ClinicalAttribute ; - sh:description "Any measurable clinical attribute." ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class diag:Quality ; - sh:description "An optional qualifier or modifier for the phenotype." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the procedure." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ] ; - sh:targetClass diag:DiagnosticProceduretoAttributeAssociation . - -diag:DiagnosticProceduretoPhenotypeAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A triple representing a relationship between a diagnostic procedure and an associated phenotype, e.g., \"blood pressure measurement\" is associated with \"high blood pressure\"." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class diag:DiagnosticProcedure ; - sh:description "A diagnostic procedure yielding a result, which in turn may be interpreted as a phenotype. Procedures include \"heart rate measurement\", \"blood pressure measurement\", \"oxygen saturation measurement\", etc. In practice, procedures may be named based on what they measure, with the \"measurement\" part left implicit." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class diag:ProcedureToPhenotypePredicate ; - sh:description "The relationship type, e.g. RELATED_TO" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class diag:Phenotype ; - sh:description "The observable physical or biochemical characteristics of a patient. Not equivalent to a disease state, but may contribute to a diagnosis." ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the procedure." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the phenotype." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ] ; - sh:targetClass diag:DiagnosticProceduretoPhenotypeAssociation . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -diag:ClinicalAttribute a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:class diag:Unit ; - sh:description "the unit used to measure the attribute" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path diag:unit ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <rdfs:label> ] ; - sh:targetClass diag:ClinicalAttribute . - -diag:Phenotype a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass diag:Phenotype . - -diag:ProcedureToAttributePredicate a sh:NodeShape ; - sh:closed true ; - sh:description "A predicate for procedure to attribute relationships, defining \"this procedure is a measurement of this attribute\"." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass diag:ProcedureToAttributePredicate . - -diag:ProcedureToPhenotypePredicate a sh:NodeShape ; - sh:closed true ; - sh:description "A predicate for procedure to phenotype relationships, defining \"this procedure is intended to provide support for/against this phenotype\"." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass diag:ProcedureToPhenotypePredicate . - -diag:Quality a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass diag:Quality . - -diag:Unit a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass diag:Unit . - -diag:DiagnosticProcedure a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass diag:DiagnosticProcedure . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/diagnostic_procedure/shex/diagnostic_procedure.shex b/projects/diagnostic_procedure/shex/diagnostic_procedure.shex deleted file mode 100644 index 13472bbc3..000000000 --- a/projects/diagnostic_procedure/shex/diagnostic_procedure.shex +++ /dev/null @@ -1,223 +0,0 @@ -BASE <http://w3id.org/ontogpt/diagnostic_procedure/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<ClinicalAttribute> CLOSED { - ( $<ClinicalAttribute_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - <unit> @<Unit> ? - ) ; - rdf:type [ <ClinicalAttribute> ] - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -<DiagnosticProcedure> CLOSED { - ( $<DiagnosticProcedure_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <DiagnosticProcedure> ] - ) -} - -<DiagnosticProceduretoAttributeAssociation> CLOSED { - ( $<DiagnosticProceduretoAttributeAssociation_tes> ( &core:Triple_tes ; - rdf:type [ core:Triple ] ? ; - <subject> @<DiagnosticProcedure> ? ; - <object> @<ClinicalAttribute> * ; - <predicate> @<ProcedureToAttributePredicate> ? ; - <subject_qualifier> @core:NamedEntity ? ; - <object_qualifier> @<Quality> ? - ) ; - rdf:type [ <DiagnosticProceduretoAttributeAssociation> ] ? - ) -} - -<DiagnosticProceduretoPhenotypeAssociation> CLOSED { - ( $<DiagnosticProceduretoPhenotypeAssociation_tes> ( &core:Triple_tes ; - rdf:type [ core:Triple ] ? ; - <subject> @<DiagnosticProcedure> ? ; - <object> @<Phenotype> * ; - <predicate> @<ProcedureToPhenotypePredicate> ? ; - <subject_qualifier> @core:NamedEntity ? ; - <object_qualifier> @core:NamedEntity ? - ) ; - rdf:type [ <DiagnosticProceduretoPhenotypeAssociation> ] ? - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -core:NamedEntity ( - @<ClinicalAttribute> OR @<DiagnosticProcedure> OR @<Phenotype> OR @<Quality> OR @core:RelationshipType OR @<Unit> -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<Phenotype> CLOSED { - ( $<Phenotype_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Phenotype> ] - ) -} - -<ProcedureToAttributePredicate> CLOSED { - ( $<ProcedureToAttributePredicate_tes> ( &core:RelationshipType_tes ; - rdf:type [ core:RelationshipType ] ? - ) ; - rdf:type [ <ProcedureToAttributePredicate> ] - ) -} - -<ProcedureToPhenotypePredicate> CLOSED { - ( $<ProcedureToPhenotypePredicate_tes> ( &core:RelationshipType_tes ; - rdf:type [ core:RelationshipType ] ? - ) ; - rdf:type [ <ProcedureToPhenotypePredicate> ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -<Quality> CLOSED { - ( $<Quality_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Quality> ] - ) -} - -core:RelationshipType ( - CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) - } OR @<ProcedureToAttributePredicate> OR @<ProcedureToPhenotypePredicate> -) - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple ( - @<DiagnosticProceduretoAttributeAssociation> OR @<DiagnosticProceduretoPhenotypeAssociation> -) - -core:Triple_struct { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - -<Unit> CLOSED { - ( $<Unit_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Unit> ] - ) -} - - diff --git a/projects/diagnostic_procedure/sqlschema/diagnostic_procedure.sql b/projects/diagnostic_procedure/sqlschema/diagnostic_procedure.sql deleted file mode 100644 index e36f64286..000000000 --- a/projects/diagnostic_procedure/sqlschema/diagnostic_procedure.sql +++ /dev/null @@ -1,109 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "DiagnosticProcedure" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Phenotype" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ProcedureToAttributePredicate" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ProcedureToPhenotypePredicate" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "Quality" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Unit" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ClinicalAttribute" ( - id TEXT NOT NULL, - label TEXT, - unit TEXT, - PRIMARY KEY (id), - FOREIGN KEY(unit) REFERENCES "Unit" (id) -); - -CREATE TABLE "DiagnosticProceduretoAttributeAssociation" ( - qualifier TEXT, - subject TEXT, - object TEXT, - predicate TEXT, - subject_qualifier TEXT, - object_qualifier TEXT, - PRIMARY KEY (qualifier, subject, object, predicate, subject_qualifier, object_qualifier), - FOREIGN KEY(subject) REFERENCES "DiagnosticProcedure" (id), - FOREIGN KEY(predicate) REFERENCES "ProcedureToAttributePredicate" (id), - FOREIGN KEY(object_qualifier) REFERENCES "Quality" (id) -); - -CREATE TABLE "DiagnosticProceduretoPhenotypeAssociation" ( - qualifier TEXT, - subject TEXT, - object TEXT, - predicate TEXT, - subject_qualifier TEXT, - object_qualifier TEXT, - PRIMARY KEY (qualifier, subject, object, predicate, subject_qualifier, object_qualifier), - FOREIGN KEY(subject) REFERENCES "DiagnosticProcedure" (id), - FOREIGN KEY(predicate) REFERENCES "ProcedureToPhenotypePredicate" (id) -); diff --git a/projects/drug/docs/AnnotatorResult.md b/projects/drug/docs/AnnotatorResult.md deleted file mode 100644 index 1ea640ba8..000000000 --- a/projects/drug/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [drug:AnnotatorResult](http://w3id.org/ontogpt/drug/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/drug/docs/Any.md b/projects/drug/docs/Any.md deleted file mode 100644 index 4da2d3785..000000000 --- a/projects/drug/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [drug:Any](http://w3id.org/ontogpt/drug/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/drug/docs/CompoundExpression.md b/projects/drug/docs/CompoundExpression.md deleted file mode 100644 index 6478dc584..000000000 --- a/projects/drug/docs/CompoundExpression.md +++ /dev/null @@ -1,21 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [drug:CompoundExpression](http://w3id.org/ontogpt/drug/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[MechanismLink],[CompoundExpression]^-[Triple],[CompoundExpression]^-[MechanismLink])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[MechanismLink],[CompoundExpression]^-[Triple],[CompoundExpression]^-[MechanismLink]) - -## Children - - * [MechanismLink](MechanismLink.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/drug/docs/Disease.md b/projects/drug/docs/Disease.md deleted file mode 100644 index 3d32596fc..000000000 --- a/projects/drug/docs/Disease.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Disease - - - - -URI: [drug:Disease](http://w3id.org/ontogpt/drug/Disease) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DrugMechanism]-%20disease%200..1>[Disease|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Disease],[DrugMechanism])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DrugMechanism]-%20disease%200..1>[Disease|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Disease],[DrugMechanism]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞disease](drugMechanism__disease.md)* <sub>0..1</sub> **[Disease](Disease.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/drug/docs/DrugMechanism.md b/projects/drug/docs/DrugMechanism.md deleted file mode 100644 index 4e2e63001..000000000 --- a/projects/drug/docs/DrugMechanism.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Class: DrugMechanism - - - - -URI: [drug:DrugMechanism](http://w3id.org/ontogpt/drug/DrugMechanism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[MechanismLink],[MechanismLink]<mechanism_links%200..*-++[DrugMechanism|references:string%20*;source_text:string%20%3F],[Drug]<drug%200..1-%20[DrugMechanism],[Disease]<disease%200..1-%20[DrugMechanism],[Drug],[Disease])](https://yuml.me/diagram/nofunky;dir:TB/class/[MechanismLink],[MechanismLink]<mechanism_links%200..*-++[DrugMechanism|references:string%20*;source_text:string%20%3F],[Drug]<drug%200..1-%20[DrugMechanism],[Disease]<disease%200..1-%20[DrugMechanism],[Drug],[Disease]) - -## Attributes - - -### Own - - * [➞disease](drugMechanism__disease.md) <sub>0..1</sub> - * Description: the name of the disease that is treated - * Range: [Disease](Disease.md) - * [➞drug](drugMechanism__drug.md) <sub>0..1</sub> - * Description: the name of the drug that treats the disease - * Range: [Drug](Drug.md) - * [➞mechanism_links](drugMechanism__mechanism_links.md) <sub>0..\*</sub> - * Description: semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type - * Range: [MechanismLink](MechanismLink.md) - * [➞references](drugMechanism__references.md) <sub>0..\*</sub> - * Range: [String](types/String.md) - * [➞source_text](drugMechanism__source_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/drug/docs/ExtractionResult.md b/projects/drug/docs/ExtractionResult.md deleted file mode 100644 index 7d07c8ae7..000000000 --- a/projects/drug/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [drug:ExtractionResult](http://w3id.org/ontogpt/drug/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/drug/docs/MechanismElement.md b/projects/drug/docs/MechanismElement.md deleted file mode 100644 index a7c61c9bd..000000000 --- a/projects/drug/docs/MechanismElement.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: MechanismElement - - - - -URI: [drug:MechanismElement](http://w3id.org/ontogpt/drug/MechanismElement) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MechanismLink]-%20object%200..1>[MechanismElement|id(i):string;label(i):string%20%3F],[MechanismLink]-%20subject%200..1>[MechanismElement],[NamedEntity]^-[MechanismElement],[MechanismLink])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MechanismLink]-%20object%200..1>[MechanismElement|id(i):string;label(i):string%20%3F],[MechanismLink]-%20subject%200..1>[MechanismElement],[NamedEntity]^-[MechanismElement],[MechanismLink]) - -## Identifier prefixes - - * HGNC - * MESH - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞object](mechanismLink__object.md)* <sub>0..1</sub> **[MechanismElement](MechanismElement.md)** - * **None** *[➞subject](mechanismLink__subject.md)* <sub>0..1</sub> **[MechanismElement](MechanismElement.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/drug/docs/MechanismLink.md b/projects/drug/docs/MechanismLink.md deleted file mode 100644 index 7f5733162..000000000 --- a/projects/drug/docs/MechanismLink.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: MechanismLink - - - - -URI: [drug:MechanismLink](http://w3id.org/ontogpt/drug/MechanismLink) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Predicate],[MechanismElement]<object%200..1-%20[MechanismLink],[Predicate]<predicate%200..1-%20[MechanismLink],[MechanismElement]<subject%200..1-%20[MechanismLink],[DrugMechanism]++-%20mechanism_links%200..*>[MechanismLink],[CompoundExpression]^-[MechanismLink],[MechanismElement],[DrugMechanism],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Predicate],[MechanismElement]<object%200..1-%20[MechanismLink],[Predicate]<predicate%200..1-%20[MechanismLink],[MechanismElement]<subject%200..1-%20[MechanismLink],[DrugMechanism]++-%20mechanism_links%200..*>[MechanismLink],[CompoundExpression]^-[MechanismLink],[MechanismElement],[DrugMechanism],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞mechanism_links](drugMechanism__mechanism_links.md)* <sub>0..\*</sub> **[MechanismLink](MechanismLink.md)** - -## Attributes - - -### Own - - * [➞subject](mechanismLink__subject.md) <sub>0..1</sub> - * Range: [MechanismElement](MechanismElement.md) - * [➞predicate](mechanismLink__predicate.md) <sub>0..1</sub> - * Range: [Predicate](Predicate.md) - * [➞object](mechanismLink__object.md) <sub>0..1</sub> - * Range: [MechanismElement](MechanismElement.md) diff --git a/projects/drug/docs/NamedEntity.md b/projects/drug/docs/NamedEntity.md deleted file mode 100644 index 4b94cf76b..000000000 --- a/projects/drug/docs/NamedEntity.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [drug:NamedEntity](http://w3id.org/ontogpt/drug/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Predicate],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Predicate],[NamedEntity]^-[MechanismElement],[NamedEntity]^-[Drug],[NamedEntity]^-[Disease],[Triple],[MechanismElement],[Drug],[Disease])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Predicate],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Predicate],[NamedEntity]^-[MechanismElement],[NamedEntity]^-[Drug],[NamedEntity]^-[Disease],[Triple],[MechanismElement],[Drug],[Disease]) - -## Children - - * [Disease](Disease.md) - * [Drug](Drug.md) - * [MechanismElement](MechanismElement.md) - * [Predicate](Predicate.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/drug/docs/NullDataOptions.md b/projects/drug/docs/NullDataOptions.md deleted file mode 100644 index 25c94dc0c..000000000 --- a/projects/drug/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [drug:NullDataOptions](http://w3id.org/ontogpt/drug/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/drug/docs/Predicate.md b/projects/drug/docs/Predicate.md deleted file mode 100644 index 6d81fd633..000000000 --- a/projects/drug/docs/Predicate.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Predicate - - - - -URI: [drug:Predicate](http://w3id.org/ontogpt/drug/Predicate) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[MechanismLink]-%20predicate%200..1>[Predicate|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Predicate],[NamedEntity],[MechanismLink])](https://yuml.me/diagram/nofunky;dir:TB/class/[MechanismLink]-%20predicate%200..1>[Predicate|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Predicate],[NamedEntity],[MechanismLink]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](mechanismLink__predicate.md)* <sub>0..1</sub> **[Predicate](Predicate.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/drug/docs/Publication.md b/projects/drug/docs/Publication.md deleted file mode 100644 index 838ef88ac..000000000 --- a/projects/drug/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [drug:Publication](http://w3id.org/ontogpt/drug/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/drug/docs/RelationshipType.md b/projects/drug/docs/RelationshipType.md deleted file mode 100644 index f59ebdaed..000000000 --- a/projects/drug/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [drug:RelationshipType](http://w3id.org/ontogpt/drug/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/drug/docs/TextWithTriples.md b/projects/drug/docs/TextWithTriples.md deleted file mode 100644 index 21688ca7d..000000000 --- a/projects/drug/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [drug:TextWithTriples](http://w3id.org/ontogpt/drug/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/drug/docs/Triple.md b/projects/drug/docs/Triple.md deleted file mode 100644 index d56fd4260..000000000 --- a/projects/drug/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [drug:Triple](http://w3id.org/ontogpt/drug/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/drug/docs/annotatorResult__object_id.md b/projects/drug/docs/annotatorResult__object_id.md deleted file mode 100644 index 3be702157..000000000 --- a/projects/drug/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [drug:annotatorResult__object_id](http://w3id.org/ontogpt/drug/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/drug/docs/annotatorResult__object_text.md b/projects/drug/docs/annotatorResult__object_text.md deleted file mode 100644 index 69b131f6a..000000000 --- a/projects/drug/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [drug:annotatorResult__object_text](http://w3id.org/ontogpt/drug/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/drug/docs/annotatorResult__subject_text.md b/projects/drug/docs/annotatorResult__subject_text.md deleted file mode 100644 index c72ea9131..000000000 --- a/projects/drug/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [drug:annotatorResult__subject_text](http://w3id.org/ontogpt/drug/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/drug/docs/drug.md b/projects/drug/docs/drug.md deleted file mode 100644 index 839797c32..000000000 --- a/projects/drug/docs/drug.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Drug - - - - -URI: [drug:Drug](http://w3id.org/ontogpt/drug/Drug) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DrugMechanism]-%20drug%200..1>[Drug|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Drug],[DrugMechanism])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DrugMechanism]-%20drug%200..1>[Drug|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Drug],[DrugMechanism]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞drug](drugMechanism__drug.md)* <sub>0..1</sub> **[Drug](Drug.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/drug/docs/drugMechanism__disease.md b/projects/drug/docs/drugMechanism__disease.md deleted file mode 100644 index aafd767bb..000000000 --- a/projects/drug/docs/drugMechanism__disease.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: disease - - -the name of the disease that is treated - -URI: [drug:drugMechanism__disease](http://w3id.org/ontogpt/drug/drugMechanism__disease) - - -## Domain and Range - -None → <sub>0..1</sub> [Disease](Disease.md) - -## Parents - - -## Children - - -## Used by - - * [DrugMechanism](DrugMechanism.md) diff --git a/projects/drug/docs/drugMechanism__drug.md b/projects/drug/docs/drugMechanism__drug.md deleted file mode 100644 index a17312acb..000000000 --- a/projects/drug/docs/drugMechanism__drug.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: drug - - -the name of the drug that treats the disease - -URI: [drug:drugMechanism__drug](http://w3id.org/ontogpt/drug/drugMechanism__drug) - - -## Domain and Range - -None → <sub>0..1</sub> [Drug](Drug.md) - -## Parents - - -## Children - - -## Used by - - * [DrugMechanism](DrugMechanism.md) diff --git a/projects/drug/docs/drugMechanism__mechanism_links.md b/projects/drug/docs/drugMechanism__mechanism_links.md deleted file mode 100644 index 9121fd44c..000000000 --- a/projects/drug/docs/drugMechanism__mechanism_links.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: mechanism_links - - -semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type - -URI: [drug:drugMechanism__mechanism_links](http://w3id.org/ontogpt/drug/drugMechanism__mechanism_links) - - -## Domain and Range - -None → <sub>0..\*</sub> [MechanismLink](MechanismLink.md) - -## Parents - - -## Children - - -## Used by - - * [DrugMechanism](DrugMechanism.md) diff --git a/projects/drug/docs/drugMechanism__references.md b/projects/drug/docs/drugMechanism__references.md deleted file mode 100644 index be2074040..000000000 --- a/projects/drug/docs/drugMechanism__references.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: references - - - - -URI: [drug:drugMechanism__references](http://w3id.org/ontogpt/drug/drugMechanism__references) - - -## Domain and Range - -None → <sub>0..\*</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [DrugMechanism](DrugMechanism.md) diff --git a/projects/drug/docs/drugMechanism__source_text.md b/projects/drug/docs/drugMechanism__source_text.md deleted file mode 100644 index 5ddd93aad..000000000 --- a/projects/drug/docs/drugMechanism__source_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: source_text - - - - -URI: [drug:drugMechanism__source_text](http://w3id.org/ontogpt/drug/drugMechanism__source_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [DrugMechanism](DrugMechanism.md) diff --git a/projects/drug/docs/extractionResult__extracted_object.md b/projects/drug/docs/extractionResult__extracted_object.md deleted file mode 100644 index 9e1ffec86..000000000 --- a/projects/drug/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [drug:extractionResult__extracted_object](http://w3id.org/ontogpt/drug/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/drug/docs/extractionResult__input_id.md b/projects/drug/docs/extractionResult__input_id.md deleted file mode 100644 index 3091924ef..000000000 --- a/projects/drug/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [drug:extractionResult__input_id](http://w3id.org/ontogpt/drug/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/drug/docs/extractionResult__input_text.md b/projects/drug/docs/extractionResult__input_text.md deleted file mode 100644 index e52590f86..000000000 --- a/projects/drug/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [drug:extractionResult__input_text](http://w3id.org/ontogpt/drug/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/drug/docs/extractionResult__input_title.md b/projects/drug/docs/extractionResult__input_title.md deleted file mode 100644 index db5911166..000000000 --- a/projects/drug/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [drug:extractionResult__input_title](http://w3id.org/ontogpt/drug/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/drug/docs/extractionResult__named_entities.md b/projects/drug/docs/extractionResult__named_entities.md deleted file mode 100644 index 5d7701c98..000000000 --- a/projects/drug/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [drug:extractionResult__named_entities](http://w3id.org/ontogpt/drug/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/drug/docs/extractionResult__prompt.md b/projects/drug/docs/extractionResult__prompt.md deleted file mode 100644 index dc94587a9..000000000 --- a/projects/drug/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [drug:extractionResult__prompt](http://w3id.org/ontogpt/drug/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/drug/docs/extractionResult__raw_completion_output.md b/projects/drug/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 1e77ca0a5..000000000 --- a/projects/drug/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [drug:extractionResult__raw_completion_output](http://w3id.org/ontogpt/drug/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/drug/docs/mechanismLink__object.md b/projects/drug/docs/mechanismLink__object.md deleted file mode 100644 index 01aff3202..000000000 --- a/projects/drug/docs/mechanismLink__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [drug:mechanismLink__object](http://w3id.org/ontogpt/drug/mechanismLink__object) - - -## Domain and Range - -None → <sub>0..1</sub> [MechanismElement](MechanismElement.md) - -## Parents - - -## Children - - -## Used by - - * [MechanismLink](MechanismLink.md) diff --git a/projects/drug/docs/mechanismLink__predicate.md b/projects/drug/docs/mechanismLink__predicate.md deleted file mode 100644 index 83bf0fd17..000000000 --- a/projects/drug/docs/mechanismLink__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [drug:mechanismLink__predicate](http://w3id.org/ontogpt/drug/mechanismLink__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [Predicate](Predicate.md) - -## Parents - - -## Children - - -## Used by - - * [MechanismLink](MechanismLink.md) diff --git a/projects/drug/docs/mechanismLink__subject.md b/projects/drug/docs/mechanismLink__subject.md deleted file mode 100644 index c1f1270ae..000000000 --- a/projects/drug/docs/mechanismLink__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [drug:mechanismLink__subject](http://w3id.org/ontogpt/drug/mechanismLink__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [MechanismElement](MechanismElement.md) - -## Parents - - -## Children - - -## Used by - - * [MechanismLink](MechanismLink.md) diff --git a/projects/drug/docs/namedEntity__id.md b/projects/drug/docs/namedEntity__id.md deleted file mode 100644 index 4cde4a702..000000000 --- a/projects/drug/docs/namedEntity__id.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [drug:namedEntity__id](http://w3id.org/ontogpt/drug/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Disease](Disease.md) - * [Drug](Drug.md) - * [MechanismElement](MechanismElement.md) - * [NamedEntity](NamedEntity.md) - * [Predicate](Predicate.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/drug/docs/namedEntity__label.md b/projects/drug/docs/namedEntity__label.md deleted file mode 100644 index ce578146f..000000000 --- a/projects/drug/docs/namedEntity__label.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [drug:namedEntity__label](http://w3id.org/ontogpt/drug/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Disease](Disease.md) - * [Drug](Drug.md) - * [MechanismElement](MechanismElement.md) - * [NamedEntity](NamedEntity.md) - * [Predicate](Predicate.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/drug/docs/publication__abstract.md b/projects/drug/docs/publication__abstract.md deleted file mode 100644 index f72aeea74..000000000 --- a/projects/drug/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [drug:publication__abstract](http://w3id.org/ontogpt/drug/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/drug/docs/publication__combined_text.md b/projects/drug/docs/publication__combined_text.md deleted file mode 100644 index 5e743fb57..000000000 --- a/projects/drug/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [drug:publication__combined_text](http://w3id.org/ontogpt/drug/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/drug/docs/publication__full_text.md b/projects/drug/docs/publication__full_text.md deleted file mode 100644 index 7612a1e21..000000000 --- a/projects/drug/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [drug:publication__full_text](http://w3id.org/ontogpt/drug/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/drug/docs/publication__id.md b/projects/drug/docs/publication__id.md deleted file mode 100644 index 6559e9615..000000000 --- a/projects/drug/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [drug:publication__id](http://w3id.org/ontogpt/drug/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/drug/docs/publication__title.md b/projects/drug/docs/publication__title.md deleted file mode 100644 index 5f67aee85..000000000 --- a/projects/drug/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [drug:publication__title](http://w3id.org/ontogpt/drug/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/drug/docs/textWithTriples__publication.md b/projects/drug/docs/textWithTriples__publication.md deleted file mode 100644 index d4cad2729..000000000 --- a/projects/drug/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [drug:textWithTriples__publication](http://w3id.org/ontogpt/drug/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/drug/docs/textWithTriples__triples.md b/projects/drug/docs/textWithTriples__triples.md deleted file mode 100644 index a8f3c7d31..000000000 --- a/projects/drug/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [drug:textWithTriples__triples](http://w3id.org/ontogpt/drug/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/drug/docs/triple__object.md b/projects/drug/docs/triple__object.md deleted file mode 100644 index a2e0c615d..000000000 --- a/projects/drug/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [drug:triple__object](http://w3id.org/ontogpt/drug/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/drug/docs/triple__object_qualifier.md b/projects/drug/docs/triple__object_qualifier.md deleted file mode 100644 index c34b7cd0b..000000000 --- a/projects/drug/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [drug:triple__object_qualifier](http://w3id.org/ontogpt/drug/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/drug/docs/triple__predicate.md b/projects/drug/docs/triple__predicate.md deleted file mode 100644 index b8c744fdf..000000000 --- a/projects/drug/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [drug:triple__predicate](http://w3id.org/ontogpt/drug/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/drug/docs/triple__qualifier.md b/projects/drug/docs/triple__qualifier.md deleted file mode 100644 index 5e6c0ade3..000000000 --- a/projects/drug/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [drug:triple__qualifier](http://w3id.org/ontogpt/drug/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/drug/docs/triple__subject.md b/projects/drug/docs/triple__subject.md deleted file mode 100644 index 13d718c66..000000000 --- a/projects/drug/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [drug:triple__subject](http://w3id.org/ontogpt/drug/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/drug/docs/triple__subject_qualifier.md b/projects/drug/docs/triple__subject_qualifier.md deleted file mode 100644 index 50842f269..000000000 --- a/projects/drug/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [drug:triple__subject_qualifier](http://w3id.org/ontogpt/drug/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/drug/docs/types/Boolean.md b/projects/drug/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/drug/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/drug/docs/types/Curie.md b/projects/drug/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/drug/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/drug/docs/types/Date.md b/projects/drug/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/drug/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/drug/docs/types/DateOrDatetime.md b/projects/drug/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/drug/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/drug/docs/types/Datetime.md b/projects/drug/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/drug/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/drug/docs/types/Decimal.md b/projects/drug/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/drug/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/drug/docs/types/Double.md b/projects/drug/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/drug/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/drug/docs/types/Float.md b/projects/drug/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/drug/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/drug/docs/types/Integer.md b/projects/drug/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/drug/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/drug/docs/types/Jsonpath.md b/projects/drug/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/drug/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/drug/docs/types/Jsonpointer.md b/projects/drug/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/drug/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/drug/docs/types/Ncname.md b/projects/drug/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/drug/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/drug/docs/types/Nodeidentifier.md b/projects/drug/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/drug/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/drug/docs/types/Objectidentifier.md b/projects/drug/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/drug/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/drug/docs/types/Sparqlpath.md b/projects/drug/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/drug/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/drug/docs/types/String.md b/projects/drug/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/drug/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/drug/docs/types/Time.md b/projects/drug/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/drug/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/drug/docs/types/Uri.md b/projects/drug/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/drug/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/drug/docs/types/Uriorcurie.md b/projects/drug/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/drug/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/drug/drug.py b/projects/drug/drug.py deleted file mode 100644 index 306776729..000000000 --- a/projects/drug/drug.py +++ /dev/null @@ -1,546 +0,0 @@ -# Auto generated from drug.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:52:51 -# Schema: drug -# -# id: http://w3id.org/ontogpt/drug -# description: A template for Drugs and drug mechanism -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -HGNC = CurieNamespace('HGNC', 'http://example.org/UNKNOWN/HGNC/') -MESH = CurieNamespace('MESH', 'http://example.org/UNKNOWN/MESH/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -DRUG = CurieNamespace('drug', 'http://w3id.org/ontogpt/drug/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = DRUG - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class MechanismElementId(NamedEntityId): - pass - - -class DiseaseId(NamedEntityId): - pass - - -class DrugId(NamedEntityId): - pass - - -class PredicateId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class DrugMechanism(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.DrugMechanism - class_class_curie: ClassVar[str] = "drug:DrugMechanism" - class_name: ClassVar[str] = "DrugMechanism" - class_model_uri: ClassVar[URIRef] = DRUG.DrugMechanism - - disease: Optional[Union[str, DiseaseId]] = None - drug: Optional[Union[str, DrugId]] = None - mechanism_links: Optional[Union[Union[dict, "MechanismLink"], List[Union[dict, "MechanismLink"]]]] = empty_list() - references: Optional[Union[str, List[str]]] = empty_list() - source_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.disease is not None and not isinstance(self.disease, DiseaseId): - self.disease = DiseaseId(self.disease) - - if self.drug is not None and not isinstance(self.drug, DrugId): - self.drug = DrugId(self.drug) - - if not isinstance(self.mechanism_links, list): - self.mechanism_links = [self.mechanism_links] if self.mechanism_links is not None else [] - self.mechanism_links = [v if isinstance(v, MechanismLink) else MechanismLink(**as_dict(v)) for v in self.mechanism_links] - - if not isinstance(self.references, list): - self.references = [self.references] if self.references is not None else [] - self.references = [v if isinstance(v, str) else str(v) for v in self.references] - - if self.source_text is not None and not isinstance(self.source_text, str): - self.source_text = str(self.source_text) - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = DRUG.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = DRUG.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class MechanismElement(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.MechanismElement - class_class_curie: ClassVar[str] = "drug:MechanismElement" - class_name: ClassVar[str] = "MechanismElement" - class_model_uri: ClassVar[URIRef] = DRUG.MechanismElement - - id: Union[str, MechanismElementId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MechanismElementId): - self.id = MechanismElementId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Disease(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.Disease - class_class_curie: ClassVar[str] = "drug:Disease" - class_name: ClassVar[str] = "Disease" - class_model_uri: ClassVar[URIRef] = DRUG.Disease - - id: Union[str, DiseaseId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiseaseId): - self.id = DiseaseId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Drug(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.Drug - class_class_curie: ClassVar[str] = "drug:Drug" - class_name: ClassVar[str] = "Drug" - class_model_uri: ClassVar[URIRef] = DRUG.Drug - - id: Union[str, DrugId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DrugId): - self.id = DrugId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Predicate(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.Predicate - class_class_curie: ClassVar[str] = "drug:Predicate" - class_name: ClassVar[str] = "Predicate" - class_model_uri: ClassVar[URIRef] = DRUG.Predicate - - id: Union[str, PredicateId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PredicateId): - self.id = PredicateId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = DRUG.CompoundExpression - - -@dataclass -class MechanismLink(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = DRUG.MechanismLink - class_class_curie: ClassVar[str] = "drug:MechanismLink" - class_name: ClassVar[str] = "MechanismLink" - class_model_uri: ClassVar[URIRef] = DRUG.MechanismLink - - subject: Optional[Union[str, MechanismElementId]] = None - predicate: Optional[Union[str, PredicateId]] = None - object: Optional[Union[str, MechanismElementId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, MechanismElementId): - self.subject = MechanismElementId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, PredicateId): - self.predicate = PredicateId(self.predicate) - - if self.object is not None and not isinstance(self.object, MechanismElementId): - self.object = MechanismElementId(self.object) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = DRUG.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = DRUG.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = DRUG.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = DRUG.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = DRUG.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.drugMechanism__disease = Slot(uri=DRUG.disease, name="drugMechanism__disease", curie=DRUG.curie('disease'), - model_uri=DRUG.drugMechanism__disease, domain=None, range=Optional[Union[str, DiseaseId]]) - -slots.drugMechanism__drug = Slot(uri=DRUG.drug, name="drugMechanism__drug", curie=DRUG.curie('drug'), - model_uri=DRUG.drugMechanism__drug, domain=None, range=Optional[Union[str, DrugId]]) - -slots.drugMechanism__mechanism_links = Slot(uri=DRUG.mechanism_links, name="drugMechanism__mechanism_links", curie=DRUG.curie('mechanism_links'), - model_uri=DRUG.drugMechanism__mechanism_links, domain=None, range=Optional[Union[Union[dict, MechanismLink], List[Union[dict, MechanismLink]]]]) - -slots.drugMechanism__references = Slot(uri=DRUG.references, name="drugMechanism__references", curie=DRUG.curie('references'), - model_uri=DRUG.drugMechanism__references, domain=None, range=Optional[Union[str, List[str]]]) - -slots.drugMechanism__source_text = Slot(uri=DRUG.source_text, name="drugMechanism__source_text", curie=DRUG.curie('source_text'), - model_uri=DRUG.drugMechanism__source_text, domain=None, range=Optional[str]) - -slots.mechanismLink__subject = Slot(uri=DRUG.subject, name="mechanismLink__subject", curie=DRUG.curie('subject'), - model_uri=DRUG.mechanismLink__subject, domain=None, range=Optional[Union[str, MechanismElementId]]) - -slots.mechanismLink__predicate = Slot(uri=DRUG.predicate, name="mechanismLink__predicate", curie=DRUG.curie('predicate'), - model_uri=DRUG.mechanismLink__predicate, domain=None, range=Optional[Union[str, PredicateId]]) - -slots.mechanismLink__object = Slot(uri=DRUG.object, name="mechanismLink__object", curie=DRUG.curie('object'), - model_uri=DRUG.mechanismLink__object, domain=None, range=Optional[Union[str, MechanismElementId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=DRUG.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=DRUG.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=DRUG.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=DRUG.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=DRUG.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=DRUG.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=DRUG.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=DRUG.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=DRUG.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=DRUG.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=DRUG.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=DRUG.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=DRUG.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=DRUG.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=DRUG.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=DRUG.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=DRUG.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=DRUG.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=DRUG.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=DRUG.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=DRUG.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=DRUG.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=DRUG.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=DRUG.annotatorResult__object_id, domain=None, range=Optional[str]) - 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zJ5K*?x#@#`J8=ppyYd3Leyu|7CAFd~1SA&J-%pr;Re%5T1>55PJ#X?*`r&zxpRxde zFGS_PO8?{Z$3yXl=OKQHkAwgI52qs@0zBLg`zL@O8aU>_0Ds&adx-LI%jOqK4cHt1 zfO225{`)8lVAA^o%KdJ{zmJlK{701g(fYrSLX7%Hl>0gHLzIVO&R=>-0<+s6p6Gt) z`4HvdnC=$}5%`GEA5iXxb`Mb=&ZvH&yukP)%KgOZA<Dxk$uAT-a7g@NE%!5%hbaH* zFF!iYf4qGCin0HQ!g}BNKZJSMxc-8n!2L7KeH;4_=3$TZ3#J1+75&3AvHsD0A2ta8 zgn^I&a~BxqSG(|V1rO`HU!r}4zg2q=1s~Q+zXU6Y{<-vjR8J3uAF}H&;Wm<c;lFV0 jL!5`q^9$z-=^uGWQ5FV#h6@0|0>8yz004t0Kfe7J!NNcZ diff --git a/projects/drug/graphql/drug.graphql b/projects/drug/graphql/drug.graphql deleted file mode 100644 index e0915eee8..000000000 --- a/projects/drug/graphql/drug.graphql +++ /dev/null @@ -1,103 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type Disease - { - id: String! - label: String - } - -type Drug - { - id: String! - label: String - } - -type DrugMechanism - { - disease: Disease - drug: Drug - mechanismLinks: [MechanismLink] - references: [String] - sourceText: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type MechanismElement - { - id: String! - label: String - } - -type MechanismLink - { - subject: MechanismElement - predicate: Predicate - object: MechanismElement - } - -interface NamedEntity - { - id: String! - label: String - } - -type Predicate - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/drug/jsonld/drug.context.jsonld b/projects/drug/jsonld/drug.context.jsonld deleted file mode 100644 index 55aab6d3c..000000000 --- a/projects/drug/jsonld/drug.context.jsonld +++ /dev/null @@ -1,137 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:52:43", - "source": "drug.yaml" - }, - "@context": { - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "MESH": "http://example.org/UNKNOWN/MESH/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "drug": { - "@type": "@id" - }, - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/drug/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "disease": { - "@type": "@id" - }, - "mechanism_links": { - "@type": "@id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/drug/jsonld/drug.jsonld b/projects/drug/jsonld/drug.jsonld deleted file mode 100644 index bacf82f23..000000000 --- a/projects/drug/jsonld/drug.jsonld +++ /dev/null @@ -1,1264 +0,0 @@ -{ - "name": "drug", - "description": "A template for Drugs and drug mechanism", - "title": "Drug Template", - "id": "http://w3id.org/ontogpt/drug", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "drug", - "prefix_reference": "http://w3id.org/ontogpt/drug/" - } - ], - "default_prefix": "drug", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "drugMechanism__disease", - "description": "the name of the disease that is treated", - "from_schema": "http://w3id.org/ontogpt/drug", - "slot_uri": "http://w3id.org/ontogpt/drug/disease", - "alias": "disease", - "owner": "DrugMechanism", - "domain_of": [ - "DrugMechanism" - ], - "range": "Disease", - "@type": "SlotDefinition" - }, - { - "name": "drugMechanism__drug", - "description": "the name of the drug that treats the disease", - "from_schema": "http://w3id.org/ontogpt/drug", - "slot_uri": "http://w3id.org/ontogpt/drug/drug", - "alias": "drug", - "owner": "DrugMechanism", - "domain_of": [ - "DrugMechanism" - ], - "range": "Drug", - "@type": "SlotDefinition" - }, - { - "name": "drugMechanism__mechanism_links", - "description": "semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type", - "from_schema": "http://w3id.org/ontogpt/drug", - "slot_uri": "http://w3id.org/ontogpt/drug/mechanism_links", - "multivalued": true, - "alias": "mechanism_links", - "owner": "DrugMechanism", - "domain_of": [ - "DrugMechanism" - ], - "range": "MechanismLink", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "drugMechanism__references", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/drug", - "slot_uri": "http://w3id.org/ontogpt/drug/references", - "multivalued": true, - "alias": "references", - "owner": "DrugMechanism", - "domain_of": [ - "DrugMechanism" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "drugMechanism__source_text", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/drug", - "slot_uri": "http://w3id.org/ontogpt/drug/source_text", - "alias": "source_text", - "owner": "DrugMechanism", - "domain_of": [ - "DrugMechanism" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "mechanismLink__subject", - "from_schema": "http://w3id.org/ontogpt/drug", - "slot_uri": "http://w3id.org/ontogpt/drug/subject", - "alias": "subject", - "owner": "MechanismLink", - "domain_of": [ - "MechanismLink" - ], - "range": "MechanismElement", - "@type": "SlotDefinition" - }, - { - "name": "mechanismLink__predicate", - "from_schema": "http://w3id.org/ontogpt/drug", - "slot_uri": "http://w3id.org/ontogpt/drug/predicate", - "alias": "predicate", - "owner": "MechanismLink", - "domain_of": [ - "MechanismLink" - ], - "range": "Predicate", - "@type": "SlotDefinition" - }, - { - "name": "mechanismLink__object", - "from_schema": "http://w3id.org/ontogpt/drug", - "slot_uri": "http://w3id.org/ontogpt/drug/object", - "alias": "object", - "owner": "MechanismLink", - "domain_of": [ - "MechanismLink" - ], - "range": "MechanismElement", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "DrugMechanism", - "definition_uri": "http://w3id.org/ontogpt/drug/DrugMechanism", - "from_schema": "http://w3id.org/ontogpt/drug", - "slots": [ - "drugMechanism__disease", - "drugMechanism__drug", - "drugMechanism__mechanism_links", - "drugMechanism__references", - "drugMechanism__source_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "disease", - "description": "the name of the disease that is treated", - "range": "Disease", - "@type": "SlotDefinition" - }, - { - "name": "drug", - "description": "the name of the drug that treats the disease", - "range": "Drug", - "@type": "SlotDefinition" - }, - { - "name": "mechanism_links", - "description": "semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type", - "multivalued": true, - "range": "MechanismLink", - "@type": "SlotDefinition" - }, - { - "name": "references", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "source_text", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/drug/DrugMechanism", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "MechanismElement", - "id_prefixes": [ - "HGNC", - "MESH" - ], - "definition_uri": "http://w3id.org/ontogpt/drug/MechanismElement", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go, sqlite:obo:mesh, sqlite:obo:uberon, sqlite:obo:pr, sqlite:obo:ncbitaxon, sqlite:obo:cl", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/drug", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/MechanismElement", - "@type": "ClassDefinition" - }, - { - "name": "Disease", - "definition_uri": "http://w3id.org/ontogpt/drug/Disease", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:mesh, sqlite:obo:mondo", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/drug", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/Disease", - "@type": "ClassDefinition" - }, - { - "name": "Drug", - "definition_uri": "http://w3id.org/ontogpt/drug/Drug", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:drugbank, sqlite:obo:chebi, sqlite:obo:mesh", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/drug", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/Drug", - "@type": "ClassDefinition" - }, - { - "name": "Predicate", - "definition_uri": "http://w3id.org/ontogpt/drug/Predicate", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:biolink, sqlite:obo:ro", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/drug", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/drug/Predicate", - "@type": "ClassDefinition" - }, - { - "name": "MechanismLink", - "definition_uri": "http://w3id.org/ontogpt/drug/MechanismLink", - "from_schema": "http://w3id.org/ontogpt/drug", - "is_a": "CompoundExpression", - "slots": [ - "mechanismLink__subject", - "mechanismLink__predicate", - "mechanismLink__object" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "MechanismElement", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "Predicate", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "MechanismElement", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/drug/MechanismLink", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "drug.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 1856, - "generation_date": "2023-08-07T10:52:43", - "@type": "SchemaDefinition", - "@context": [ - "projects/drug/jsonld/drug.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/drug/" - } - ] -} diff --git a/projects/drug/jsonschema/drug.schema.json b/projects/drug/jsonschema/drug.schema.json deleted file mode 100644 index 46c9c9bf6..000000000 --- a/projects/drug/jsonschema/drug.schema.json +++ /dev/null @@ -1,292 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "Disease": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Disease", - "type": "object" - }, - "Drug": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Drug", - "type": "object" - }, - "DrugMechanism": { - "additionalProperties": false, - "description": "", - "properties": { - "disease": { - "description": "the name of the disease that is treated", - "type": "string" - }, - "drug": { - "description": "the name of the drug that treats the disease", - "type": "string" - }, - "mechanism_links": { - "description": "semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type", - "items": { - "$ref": "#/$defs/MechanismLink" - }, - "type": "array" - }, - "references": { - "items": { - "type": "string" - }, - "type": "array" - }, - "source_text": { - "type": "string" - } - }, - "title": "DrugMechanism", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "MechanismElement": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "MechanismElement", - "type": "object" - }, - "MechanismLink": { - "additionalProperties": false, - "description": "", - "properties": { - "object": { - "type": "string" - }, - "predicate": { - "type": "string" - }, - "subject": { - "type": "string" - } - }, - "title": "MechanismLink", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Predicate": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Predicate", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/drug", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "disease": { - "description": "the name of the disease that is treated", - "type": "string" - }, - "drug": { - "description": "the name of the drug that treats the disease", - "type": "string" - }, - "mechanism_links": { - "description": "semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type", - "items": { - "$ref": "#/$defs/MechanismLink" - }, - "type": "array" - }, - "references": { - "items": { - "type": "string" - }, - "type": "array" - }, - "source_text": { - "type": "string" - } - }, - "title": "drug", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/drug/owl/drug.owl.ttl b/projects/drug/owl/drug.owl.ttl deleted file mode 100644 index 6fce7c4b0..000000000 --- a/projects/drug/owl/drug.owl.ttl +++ /dev/null @@ -1,473 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix drug: <http://w3id.org/ontogpt/drug/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/drug> a owl:Ontology ; - rdfs:label "drug" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - drug:DrugMechanism ; - linkml:classes "{'DrugMechanism': ClassDefinition(name='DrugMechanism', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/DrugMechanism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/drug', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['drugMechanism__disease', 'drugMechanism__drug', 'drugMechanism__mechanism_links', 'drugMechanism__references', 'drugMechanism__source_text'], slot_usage={}, attributes={'disease': SlotDefinition(name='disease', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the disease that is treated', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'drug': SlotDefinition(name='drug', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the drug that treats the disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Drug', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'mechanism_links': SlotDefinition(name='mechanism_links', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MechanismLink', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'references': SlotDefinition(name='references', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'source_text': SlotDefinition(name='source_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='drug:DrugMechanism', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'MechanismElement': ClassDefinition(name='MechanismElement', id_prefixes=['HGNC', 'MESH'], definition_uri='http://w3id.org/ontogpt/drug/MechanismElement', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:mesh, sqlite:obo:uberon, sqlite:obo:pr, sqlite:obo:ncbitaxon, sqlite:obo:cl', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/drug', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='drug:MechanismElement', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Disease': ClassDefinition(name='Disease', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/Disease', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:mesh, sqlite:obo:mondo', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/drug', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='drug:Disease', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Drug': ClassDefinition(name='Drug', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/Drug', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:drugbank, sqlite:obo:chebi, sqlite:obo:mesh', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/drug', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='drug:Drug', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Predicate': ClassDefinition(name='Predicate', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/Predicate', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:biolink, sqlite:obo:ro', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/drug', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='drug:Predicate', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'MechanismLink': ClassDefinition(name='MechanismLink', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/drug/MechanismLink', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/drug', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['mechanismLink__subject', 'mechanismLink__predicate', 'mechanismLink__object'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MechanismElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Predicate', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MechanismElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='drug:MechanismLink', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/drug" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - drug:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -drug:DrugMechanism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DrugMechanism" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom drug:MechanismLink ; - owl:onProperty drug:mechanism_links ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass drug:Disease ; - owl:onProperty drug:disease ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass drug:Drug ; - owl:onProperty drug:drug ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty drug:source_text ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty drug:references ] ; - linkml:attributes "{'disease': SlotDefinition(name='disease', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the disease that is treated', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'drug': SlotDefinition(name='drug', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the drug that treats the disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Drug', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'mechanism_links': SlotDefinition(name='mechanism_links', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MechanismLink', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'references': SlotDefinition(name='references', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'source_text': SlotDefinition(name='source_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -drug:disease a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "disease" ; - rdfs:range drug:Disease ; - skos:definition "the name of the disease that is treated" . - -drug:drug a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "drug" ; - rdfs:range drug:Drug ; - skos:definition "the name of the drug that treats the disease" . - -drug:mechanism_links a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "mechanism_links" ; - rdfs:range drug:MechanismLink ; - skos:definition "semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type" . - -drug:object a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range drug:MechanismElement . - -drug:predicate a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range drug:Predicate . - -drug:references a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "references" ; - drug:prompt.skip "true" ; - rdfs:range linkml:String . - -drug:source_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "source_text" ; - drug:prompt.skip "true" ; - rdfs:range linkml:String . - -drug:subject a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range drug:MechanismElement . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - drug:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -drug:Disease a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Disease" ; - drug:annotators "sqlite:obo:mesh, sqlite:obo:mondo" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -drug:Drug a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Drug" ; - drug:annotators "sqlite:obo:drugbank, sqlite:obo:chebi, sqlite:obo:mesh" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -drug:MechanismLink a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MechanismLink" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass drug:MechanismElement ; - owl:onProperty drug:object ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass drug:Predicate ; - owl:onProperty drug:predicate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass drug:MechanismElement ; - owl:onProperty drug:subject ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MechanismElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Predicate', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MechanismElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -drug:Predicate a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Predicate" ; - drug:annotators "sqlite:obo:biolink, sqlite:obo:ro" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -drug:MechanismElement a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MechanismElement" ; - drug:annotators "sqlite:obo:go, sqlite:obo:mesh, sqlite:obo:uberon, sqlite:obo:pr, sqlite:obo:ncbitaxon, sqlite:obo:cl" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/drug/prefixmap/drug.yaml b/projects/drug/prefixmap/drug.yaml deleted file mode 100644 index bda25fa94..000000000 --- a/projects/drug/prefixmap/drug.yaml +++ /dev/null @@ -1,37 +0,0 @@ -{ - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "MESH": "http://example.org/UNKNOWN/MESH/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "drug": "http://w3id.org/ontogpt/drug/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/drug/protobuf/drug.proto b/projects/drug/protobuf/drug.proto deleted file mode 100644 index fa063bf0e..000000000 --- a/projects/drug/protobuf/drug.proto +++ /dev/null @@ -1,69 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message Disease - { - string id = 0 - string label = 0 - } -message Drug - { - string id = 0 - string label = 0 - } -message DrugMechanism - { - disease disease = 0 - drug drug = 0 - repeated mechanismLink mechanismLinks = 0 - repeated string references = 0 - string sourceText = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message MechanismElement - { - string id = 0 - string label = 0 - } -message MechanismLink - { - mechanismElement subject = 0 - predicate predicate = 0 - mechanismElement object = 0 - } -message Predicate - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/drug/shacl/drug.shacl.ttl b/projects/drug/shacl/drug.shacl.ttl deleted file mode 100644 index fd3029861..000000000 --- a/projects/drug/shacl/drug.shacl.ttl +++ /dev/null @@ -1,267 +0,0 @@ -@prefix drug: <http://w3id.org/ontogpt/drug/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ], - [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -drug:DrugMechanism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class drug:Drug ; - sh:description "the name of the drug that treats the disease" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path drug:drug ], - [ sh:class drug:Disease ; - sh:description "the name of the disease that is treated" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path drug:disease ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path drug:source_text ], - [ sh:order 3 ; - sh:path drug:references ], - [ sh:class drug:MechanismLink ; - sh:description "semicolon-separated list of links, where each link is a triple connecting two entities via a relationship type" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path drug:mechanism_links ] ; - sh:targetClass drug:DrugMechanism . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -drug:Disease a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass drug:Disease . - -drug:Drug a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass drug:Drug . - -drug:MechanismLink a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class drug:MechanismElement ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path drug:object ], - [ sh:class drug:Predicate ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path drug:predicate ], - [ sh:class drug:MechanismElement ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path drug:subject ] ; - sh:targetClass drug:MechanismLink . - -drug:Predicate a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass drug:Predicate . - -drug:MechanismElement a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass drug:MechanismElement . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/drug/shex/drug.shex b/projects/drug/shex/drug.shex deleted file mode 100644 index 00f492f4d..000000000 --- a/projects/drug/shex/drug.shex +++ /dev/null @@ -1,190 +0,0 @@ -BASE <http://w3id.org/ontogpt/drug/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - @<MechanismLink> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -<Disease> CLOSED { - ( $<Disease_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Disease> ] - ) -} - -<Drug> CLOSED { - ( $<Drug_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Drug> ] - ) -} - -<DrugMechanism> CLOSED { - ( $<DrugMechanism_tes> ( <disease> @<Disease> ? ; - <drug> @<Drug> ? ; - <mechanism_links> @<MechanismLink> * ; - <references> @linkml:String * ; - <source_text> @linkml:String ? - ) ; - rdf:type [ <DrugMechanism> ] ? - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<MechanismElement> CLOSED { - ( $<MechanismElement_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <MechanismElement> ] - ) -} - -<MechanismLink> CLOSED { - ( $<MechanismLink_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <subject> @<MechanismElement> ? ; - <predicate> @<Predicate> ? ; - <object> @<MechanismElement> ? - ) ; - rdf:type [ <MechanismLink> ] ? - ) -} - -core:NamedEntity ( - @<Disease> OR @<Drug> OR @<MechanismElement> OR @<Predicate> OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<Predicate> CLOSED { - ( $<Predicate_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Predicate> ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/drug/sqlschema/drug.sql b/projects/drug/sqlschema/drug.sql deleted file mode 100644 index ab9ffe6b0..000000000 --- a/projects/drug/sqlschema/drug.sql +++ /dev/null @@ -1,85 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Disease" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Drug" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "MechanismElement" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Predicate" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "DrugMechanism" ( - disease TEXT, - drug TEXT, - mechanism_links TEXT, - "references" TEXT, - source_text TEXT, - PRIMARY KEY (disease, drug, mechanism_links, "references", source_text), - FOREIGN KEY(disease) REFERENCES "Disease" (id), - FOREIGN KEY(drug) REFERENCES "Drug" (id) -); - -CREATE TABLE "MechanismLink" ( - subject TEXT, - predicate TEXT, - object TEXT, - PRIMARY KEY (subject, predicate, object), - FOREIGN KEY(subject) REFERENCES "MechanismElement" (id), - FOREIGN KEY(predicate) REFERENCES "Predicate" (id), - FOREIGN KEY(object) REFERENCES "MechanismElement" (id) -); diff --git a/projects/environmental_metadata/docs/AnnotatorResult.md b/projects/environmental_metadata/docs/AnnotatorResult.md deleted file mode 100644 index 6060db730..000000000 --- a/projects/environmental_metadata/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [envmd:AnnotatorResult](http://w3id.org/ontogpt/environmental-metadataAnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/Any.md b/projects/environmental_metadata/docs/Any.md deleted file mode 100644 index e42f52283..000000000 --- a/projects/environmental_metadata/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [envmd:Any](http://w3id.org/ontogpt/environmental-metadataAny) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/environmental_metadata/docs/CompoundExpression.md b/projects/environmental_metadata/docs/CompoundExpression.md deleted file mode 100644 index eff1887aa..000000000 --- a/projects/environmental_metadata/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [envmd:CompoundExpression](http://w3id.org/ontogpt/environmental-metadataCompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/environmental_metadata/docs/Dataset.md b/projects/environmental_metadata/docs/Dataset.md deleted file mode 100644 index d54b0e9e2..000000000 --- a/projects/environmental_metadata/docs/Dataset.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Class: Dataset - - - - -URI: [envmd:Dataset](http://w3id.org/ontogpt/environmental-metadataDataset) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Topic],[Method],[Location],[EnvironmentalMaterial],[Environment],[Method]<methods%200..*-%20[Dataset|packageid:string%20%3F],[Environment]<environments%200..*-%20[Dataset],[EnvironmentalMaterial]<environmental_material%200..*-%20[Dataset],[Location]<location%200..*-%20[Dataset],[Topic]<topic%200..*-%20[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[Topic],[Method],[Location],[EnvironmentalMaterial],[Environment],[Method]<methods%200..*-%20[Dataset|packageid:string%20%3F],[Environment]<environments%200..*-%20[Dataset],[EnvironmentalMaterial]<environmental_material%200..*-%20[Dataset],[Location]<location%200..*-%20[Dataset],[Topic]<topic%200..*-%20[Dataset]) - -## Attributes - - -### Own - - * [➞packageid](dataset__packageid.md) <sub>0..1</sub> - * Description: The internal identifier for the dataset - * Range: [String](types/String.md) - * [➞topic](dataset__topic.md) <sub>0..\*</sub> - * Description: the general scientific area of study concerning the sample(s) - * Range: [Topic](Topic.md) - * [➞location](dataset__location.md) <sub>0..\*</sub> - * Description: the geographic location where the sample was isolated - * Range: [Location](Location.md) - * [➞environmental_material](dataset__environmental_material.md) <sub>0..\*</sub> - * Description: the environmental material that was sampled - * Range: [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [➞environments](dataset__environments.md) <sub>0..\*</sub> - * Description: the environmental context in which the study was conducted - * Range: [Environment](Environment.md) - * [➞methods](dataset__methods.md) <sub>0..\*</sub> - * Range: [Method](Method.md) diff --git a/projects/environmental_metadata/docs/Environment.md b/projects/environmental_metadata/docs/Environment.md deleted file mode 100644 index 851d23f7a..000000000 --- a/projects/environmental_metadata/docs/Environment.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Environment - - - - -URI: [envmd:Environment](http://w3id.org/ontogpt/environmental-metadataEnvironment) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Dataset]-%20environments%200..*>[Environment|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Environment],[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Dataset]-%20environments%200..*>[Environment|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Environment],[Dataset]) - -## Identifier prefixes - - * ENVO - * ENVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞environments](dataset__environments.md)* <sub>0..\*</sub> **[Environment](Environment.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/EnvironmentalMaterial.md b/projects/environmental_metadata/docs/EnvironmentalMaterial.md deleted file mode 100644 index 79a2834c0..000000000 --- a/projects/environmental_metadata/docs/EnvironmentalMaterial.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: EnvironmentalMaterial - - - - -URI: [envmd:EnvironmentalMaterial](http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Dataset]-%20environmental_material%200..*>[EnvironmentalMaterial|id(i):string;label(i):string%20%3F],[NamedEntity]^-[EnvironmentalMaterial],[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Dataset]-%20environmental_material%200..*>[EnvironmentalMaterial|id(i):string;label(i):string%20%3F],[NamedEntity]^-[EnvironmentalMaterial],[Dataset]) - -## Identifier prefixes - - * ENVO - * ENVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞environmental_material](dataset__environmental_material.md)* <sub>0..\*</sub> **[EnvironmentalMaterial](EnvironmentalMaterial.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/ExtractionResult.md b/projects/environmental_metadata/docs/ExtractionResult.md deleted file mode 100644 index e390e42ee..000000000 --- a/projects/environmental_metadata/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [envmd:ExtractionResult](http://w3id.org/ontogpt/environmental-metadataExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/environmental_metadata/docs/Location.md b/projects/environmental_metadata/docs/Location.md deleted file mode 100644 index 10fcdee28..000000000 --- a/projects/environmental_metadata/docs/Location.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Location - - - - -URI: [envmd:Location](http://w3id.org/ontogpt/environmental-metadataLocation) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Dataset]-%20location%200..*>[Location|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Location],[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Dataset]-%20location%200..*>[Location|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Location],[Dataset]) - -## Identifier prefixes - - * ENVO - * GAZ - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞location](dataset__location.md)* <sub>0..\*</sub> **[Location](Location.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/Method.md b/projects/environmental_metadata/docs/Method.md deleted file mode 100644 index dec9980fb..000000000 --- a/projects/environmental_metadata/docs/Method.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Method - - - - -URI: [envmd:Method](http://w3id.org/ontogpt/environmental-metadataMethod) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Dataset]-%20methods%200..*>[Method|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Method],[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Dataset]-%20methods%200..*>[Method|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Method],[Dataset]) - -## Identifier prefixes - - * ENVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞methods](dataset__methods.md)* <sub>0..\*</sub> **[Method](Method.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/NamedEntity.md b/projects/environmental_metadata/docs/NamedEntity.md deleted file mode 100644 index 1c075c09f..000000000 --- a/projects/environmental_metadata/docs/NamedEntity.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [envmd:NamedEntity](http://w3id.org/ontogpt/environmental-metadataNamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Topic],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Topic],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Method],[NamedEntity]^-[Location],[NamedEntity]^-[EnvironmentalMaterial],[NamedEntity]^-[Environment],[Triple],[Method],[Location],[EnvironmentalMaterial],[Environment])](https://yuml.me/diagram/nofunky;dir:TB/class/[Topic],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Topic],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Method],[NamedEntity]^-[Location],[NamedEntity]^-[EnvironmentalMaterial],[NamedEntity]^-[Environment],[Triple],[Method],[Location],[EnvironmentalMaterial],[Environment]) - -## Children - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [Method](Method.md) - * [RelationshipType](RelationshipType.md) - * [Topic](Topic.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/NullDataOptions.md b/projects/environmental_metadata/docs/NullDataOptions.md deleted file mode 100644 index 25a33076d..000000000 --- a/projects/environmental_metadata/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [envmd:NullDataOptions](http://w3id.org/ontogpt/environmental-metadataNullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/environmental_metadata/docs/Publication.md b/projects/environmental_metadata/docs/Publication.md deleted file mode 100644 index 46dd3ee50..000000000 --- a/projects/environmental_metadata/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [envmd:Publication](http://w3id.org/ontogpt/environmental-metadataPublication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/RelationshipType.md b/projects/environmental_metadata/docs/RelationshipType.md deleted file mode 100644 index 3145f0773..000000000 --- a/projects/environmental_metadata/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [envmd:RelationshipType](http://w3id.org/ontogpt/environmental-metadataRelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/TextWithTriples.md b/projects/environmental_metadata/docs/TextWithTriples.md deleted file mode 100644 index e67af9874..000000000 --- a/projects/environmental_metadata/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [envmd:TextWithTriples](http://w3id.org/ontogpt/environmental-metadataTextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/environmental_metadata/docs/Topic.md b/projects/environmental_metadata/docs/Topic.md deleted file mode 100644 index 01162867d..000000000 --- a/projects/environmental_metadata/docs/Topic.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Topic - - - - -URI: [envmd:Topic](http://w3id.org/ontogpt/environmental-metadataTopic) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Dataset]-%20topic%200..*>[Topic|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Topic],[NamedEntity],[Dataset])](https://yuml.me/diagram/nofunky;dir:TB/class/[Dataset]-%20topic%200..*>[Topic|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Topic],[NamedEntity],[Dataset]) - -## Identifier prefixes - - * ENVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞topic](dataset__topic.md)* <sub>0..\*</sub> **[Topic](Topic.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_metadata/docs/Triple.md b/projects/environmental_metadata/docs/Triple.md deleted file mode 100644 index afeb4ff25..000000000 --- a/projects/environmental_metadata/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [envmd:Triple](http://w3id.org/ontogpt/environmental-metadataTriple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/environmental_metadata/docs/annotatorResult__object_id.md b/projects/environmental_metadata/docs/annotatorResult__object_id.md deleted file mode 100644 index 918a3ec02..000000000 --- a/projects/environmental_metadata/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [envmd:annotatorResult__object_id](http://w3id.org/ontogpt/environmental-metadataannotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/environmental_metadata/docs/annotatorResult__object_text.md b/projects/environmental_metadata/docs/annotatorResult__object_text.md deleted file mode 100644 index 7c75cb72f..000000000 --- a/projects/environmental_metadata/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [envmd:annotatorResult__object_text](http://w3id.org/ontogpt/environmental-metadataannotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/environmental_metadata/docs/annotatorResult__subject_text.md b/projects/environmental_metadata/docs/annotatorResult__subject_text.md deleted file mode 100644 index 4fadfa223..000000000 --- a/projects/environmental_metadata/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [envmd:annotatorResult__subject_text](http://w3id.org/ontogpt/environmental-metadataannotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/environmental_metadata/docs/dataset__environmental_material.md b/projects/environmental_metadata/docs/dataset__environmental_material.md deleted file mode 100644 index c3140a16b..000000000 --- a/projects/environmental_metadata/docs/dataset__environmental_material.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: environmental_material - - -the environmental material that was sampled - -URI: [envmd:dataset__environmental_material](http://w3id.org/ontogpt/environmental-metadatadataset__environmental_material) - - -## Domain and Range - -None → <sub>0..\*</sub> [EnvironmentalMaterial](EnvironmentalMaterial.md) - -## Parents - - -## Children - - -## Used by - - * [Dataset](Dataset.md) diff --git a/projects/environmental_metadata/docs/dataset__environments.md b/projects/environmental_metadata/docs/dataset__environments.md deleted file mode 100644 index b721c3c1c..000000000 --- a/projects/environmental_metadata/docs/dataset__environments.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: environments - - -the environmental context in which the study was conducted - -URI: [envmd:dataset__environments](http://w3id.org/ontogpt/environmental-metadatadataset__environments) - - -## Domain and Range - -None → <sub>0..\*</sub> [Environment](Environment.md) - -## Parents - - -## Children - - -## Used by - - * [Dataset](Dataset.md) diff --git a/projects/environmental_metadata/docs/dataset__location.md b/projects/environmental_metadata/docs/dataset__location.md deleted file mode 100644 index 25e4348c9..000000000 --- a/projects/environmental_metadata/docs/dataset__location.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: location - - -the geographic location where the sample was isolated - -URI: [envmd:dataset__location](http://w3id.org/ontogpt/environmental-metadatadataset__location) - - -## Domain and Range - -None → <sub>0..\*</sub> [Location](Location.md) - -## Parents - - -## Children - - -## Used by - - * [Dataset](Dataset.md) diff --git a/projects/environmental_metadata/docs/dataset__methods.md b/projects/environmental_metadata/docs/dataset__methods.md deleted file mode 100644 index 6917e6adb..000000000 --- a/projects/environmental_metadata/docs/dataset__methods.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: methods - - - - -URI: [envmd:dataset__methods](http://w3id.org/ontogpt/environmental-metadatadataset__methods) - - -## Domain and Range - -None → <sub>0..\*</sub> [Method](Method.md) - -## Parents - - -## Children - - -## Used by - - * [Dataset](Dataset.md) diff --git a/projects/environmental_metadata/docs/dataset__packageid.md b/projects/environmental_metadata/docs/dataset__packageid.md deleted file mode 100644 index 892be96ae..000000000 --- a/projects/environmental_metadata/docs/dataset__packageid.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: packageid - - -The internal identifier for the dataset - -URI: [envmd:dataset__packageid](http://w3id.org/ontogpt/environmental-metadatadataset__packageid) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Dataset](Dataset.md) diff --git a/projects/environmental_metadata/docs/dataset__topic.md b/projects/environmental_metadata/docs/dataset__topic.md deleted file mode 100644 index c14c6d825..000000000 --- a/projects/environmental_metadata/docs/dataset__topic.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: topic - - -the general scientific area of study concerning the sample(s) - -URI: [envmd:dataset__topic](http://w3id.org/ontogpt/environmental-metadatadataset__topic) - - -## Domain and Range - -None → <sub>0..\*</sub> [Topic](Topic.md) - -## Parents - - -## Children - - -## Used by - - * [Dataset](Dataset.md) diff --git a/projects/environmental_metadata/docs/environmental_metadata.md b/projects/environmental_metadata/docs/environmental_metadata.md deleted file mode 100644 index ece03a5d6..000000000 --- a/projects/environmental_metadata/docs/environmental_metadata.md +++ /dev/null @@ -1,115 +0,0 @@ - -# environmental-metadata - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for categorizing Environmental Data Initiative data entries. See https://github.com/EDIorg/EDIorg-repository-index - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [Dataset](Dataset.md) - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [Method](Method.md) - * [RelationshipType](RelationshipType.md) - * [Topic](Topic.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞environmental_material](dataset__environmental_material.md) - the environmental material that was sampled - * [➞environments](dataset__environments.md) - the environmental context in which the study was conducted - * [➞location](dataset__location.md) - the geographic location where the sample was isolated - * [➞methods](dataset__methods.md) - * [➞packageid](dataset__packageid.md) - The internal identifier for the dataset - * [➞topic](dataset__topic.md) - the general scientific area of study concerning the sample(s) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/environmental_metadata/docs/extractionResult__extracted_object.md b/projects/environmental_metadata/docs/extractionResult__extracted_object.md deleted file mode 100644 index c6f5f2ff0..000000000 --- a/projects/environmental_metadata/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [envmd:extractionResult__extracted_object](http://w3id.org/ontogpt/environmental-metadataextractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_metadata/docs/extractionResult__input_id.md b/projects/environmental_metadata/docs/extractionResult__input_id.md deleted file mode 100644 index 4d84e2add..000000000 --- a/projects/environmental_metadata/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [envmd:extractionResult__input_id](http://w3id.org/ontogpt/environmental-metadataextractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_metadata/docs/extractionResult__input_text.md b/projects/environmental_metadata/docs/extractionResult__input_text.md deleted file mode 100644 index 542145654..000000000 --- a/projects/environmental_metadata/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [envmd:extractionResult__input_text](http://w3id.org/ontogpt/environmental-metadataextractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_metadata/docs/extractionResult__input_title.md b/projects/environmental_metadata/docs/extractionResult__input_title.md deleted file mode 100644 index b3df32354..000000000 --- a/projects/environmental_metadata/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [envmd:extractionResult__input_title](http://w3id.org/ontogpt/environmental-metadataextractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_metadata/docs/extractionResult__named_entities.md b/projects/environmental_metadata/docs/extractionResult__named_entities.md deleted file mode 100644 index f24f0474b..000000000 --- a/projects/environmental_metadata/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [envmd:extractionResult__named_entities](http://w3id.org/ontogpt/environmental-metadataextractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_metadata/docs/extractionResult__prompt.md b/projects/environmental_metadata/docs/extractionResult__prompt.md deleted file mode 100644 index e1ee7b2f6..000000000 --- a/projects/environmental_metadata/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [envmd:extractionResult__prompt](http://w3id.org/ontogpt/environmental-metadataextractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_metadata/docs/extractionResult__raw_completion_output.md b/projects/environmental_metadata/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index f586d0a1a..000000000 --- a/projects/environmental_metadata/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [envmd:extractionResult__raw_completion_output](http://w3id.org/ontogpt/environmental-metadataextractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_metadata/docs/namedEntity__id.md b/projects/environmental_metadata/docs/namedEntity__id.md deleted file mode 100644 index 6f78c52a8..000000000 --- a/projects/environmental_metadata/docs/namedEntity__id.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [envmd:namedEntity__id](http://w3id.org/ontogpt/environmental-metadatanamedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [Method](Method.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Topic](Topic.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/environmental_metadata/docs/namedEntity__label.md b/projects/environmental_metadata/docs/namedEntity__label.md deleted file mode 100644 index 49ba1372c..000000000 --- a/projects/environmental_metadata/docs/namedEntity__label.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [envmd:namedEntity__label](http://w3id.org/ontogpt/environmental-metadatanamedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [Method](Method.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Topic](Topic.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/environmental_metadata/docs/publication__abstract.md b/projects/environmental_metadata/docs/publication__abstract.md deleted file mode 100644 index 42f059d76..000000000 --- a/projects/environmental_metadata/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [envmd:publication__abstract](http://w3id.org/ontogpt/environmental-metadatapublication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_metadata/docs/publication__combined_text.md b/projects/environmental_metadata/docs/publication__combined_text.md deleted file mode 100644 index c0c440dda..000000000 --- a/projects/environmental_metadata/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [envmd:publication__combined_text](http://w3id.org/ontogpt/environmental-metadatapublication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_metadata/docs/publication__full_text.md b/projects/environmental_metadata/docs/publication__full_text.md deleted file mode 100644 index 765dac52b..000000000 --- a/projects/environmental_metadata/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [envmd:publication__full_text](http://w3id.org/ontogpt/environmental-metadatapublication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_metadata/docs/publication__id.md b/projects/environmental_metadata/docs/publication__id.md deleted file mode 100644 index 14fcd1d7e..000000000 --- a/projects/environmental_metadata/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [envmd:publication__id](http://w3id.org/ontogpt/environmental-metadatapublication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_metadata/docs/publication__title.md b/projects/environmental_metadata/docs/publication__title.md deleted file mode 100644 index d821363aa..000000000 --- a/projects/environmental_metadata/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [envmd:publication__title](http://w3id.org/ontogpt/environmental-metadatapublication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_metadata/docs/textWithTriples__publication.md b/projects/environmental_metadata/docs/textWithTriples__publication.md deleted file mode 100644 index d10a4d087..000000000 --- a/projects/environmental_metadata/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [envmd:textWithTriples__publication](http://w3id.org/ontogpt/environmental-metadatatextWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/environmental_metadata/docs/textWithTriples__triples.md b/projects/environmental_metadata/docs/textWithTriples__triples.md deleted file mode 100644 index 9a47988e7..000000000 --- a/projects/environmental_metadata/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [envmd:textWithTriples__triples](http://w3id.org/ontogpt/environmental-metadatatextWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/environmental_metadata/docs/triple__object.md b/projects/environmental_metadata/docs/triple__object.md deleted file mode 100644 index 8034d4a8f..000000000 --- a/projects/environmental_metadata/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [envmd:triple__object](http://w3id.org/ontogpt/environmental-metadatatriple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_metadata/docs/triple__object_qualifier.md b/projects/environmental_metadata/docs/triple__object_qualifier.md deleted file mode 100644 index d89d30add..000000000 --- a/projects/environmental_metadata/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [envmd:triple__object_qualifier](http://w3id.org/ontogpt/environmental-metadatatriple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_metadata/docs/triple__predicate.md b/projects/environmental_metadata/docs/triple__predicate.md deleted file mode 100644 index 465230d47..000000000 --- a/projects/environmental_metadata/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [envmd:triple__predicate](http://w3id.org/ontogpt/environmental-metadatatriple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_metadata/docs/triple__qualifier.md b/projects/environmental_metadata/docs/triple__qualifier.md deleted file mode 100644 index 0f0a895af..000000000 --- a/projects/environmental_metadata/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [envmd:triple__qualifier](http://w3id.org/ontogpt/environmental-metadatatriple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_metadata/docs/triple__subject.md b/projects/environmental_metadata/docs/triple__subject.md deleted file mode 100644 index 496fbcfc0..000000000 --- a/projects/environmental_metadata/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [envmd:triple__subject](http://w3id.org/ontogpt/environmental-metadatatriple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_metadata/docs/triple__subject_qualifier.md b/projects/environmental_metadata/docs/triple__subject_qualifier.md deleted file mode 100644 index 57598e405..000000000 --- a/projects/environmental_metadata/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [envmd:triple__subject_qualifier](http://w3id.org/ontogpt/environmental-metadatatriple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_metadata/docs/types/Boolean.md b/projects/environmental_metadata/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/environmental_metadata/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/environmental_metadata/docs/types/Curie.md b/projects/environmental_metadata/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/environmental_metadata/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/environmental_metadata/docs/types/Date.md b/projects/environmental_metadata/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/environmental_metadata/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/environmental_metadata/docs/types/DateOrDatetime.md b/projects/environmental_metadata/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/environmental_metadata/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/environmental_metadata/docs/types/Datetime.md b/projects/environmental_metadata/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/environmental_metadata/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/environmental_metadata/docs/types/Decimal.md b/projects/environmental_metadata/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/environmental_metadata/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/environmental_metadata/docs/types/Double.md b/projects/environmental_metadata/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/environmental_metadata/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/environmental_metadata/docs/types/Float.md b/projects/environmental_metadata/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/environmental_metadata/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/environmental_metadata/docs/types/Integer.md b/projects/environmental_metadata/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/environmental_metadata/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/environmental_metadata/docs/types/Jsonpath.md b/projects/environmental_metadata/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/environmental_metadata/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/environmental_metadata/docs/types/Jsonpointer.md b/projects/environmental_metadata/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/environmental_metadata/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/environmental_metadata/docs/types/Ncname.md b/projects/environmental_metadata/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/environmental_metadata/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/environmental_metadata/docs/types/Nodeidentifier.md b/projects/environmental_metadata/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/environmental_metadata/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/environmental_metadata/docs/types/Objectidentifier.md b/projects/environmental_metadata/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/environmental_metadata/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/environmental_metadata/docs/types/Sparqlpath.md b/projects/environmental_metadata/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/environmental_metadata/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/environmental_metadata/docs/types/String.md b/projects/environmental_metadata/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/environmental_metadata/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/environmental_metadata/docs/types/Time.md b/projects/environmental_metadata/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/environmental_metadata/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/environmental_metadata/docs/types/Uri.md b/projects/environmental_metadata/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/environmental_metadata/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/environmental_metadata/docs/types/Uriorcurie.md b/projects/environmental_metadata/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/environmental_metadata/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/environmental_metadata/environmental_metadata.py b/projects/environmental_metadata/environmental_metadata.py deleted file mode 100644 index c1dbceb02..000000000 --- a/projects/environmental_metadata/environmental_metadata.py +++ /dev/null @@ -1,547 +0,0 @@ -# Auto generated from environmental_metadata.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:53:05 -# Schema: environmental-metadata -# -# id: http://w3id.org/ontogpt/environmental-metadata -# description: A template for categorizing Environmental Data Initiative data entries. See -# https://github.com/EDIorg/EDIorg-repository-index -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -ENVO = CurieNamespace('ENVO', 'http://example.org/UNKNOWN/ENVO/') -ENVTHES = CurieNamespace('ENVTHES', 'http://example.org/UNKNOWN/ENVTHES/') -GAZ = CurieNamespace('GAZ', 'http://example.org/UNKNOWN/GAZ/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -ENVMD = CurieNamespace('envmd', 'http://w3id.org/ontogpt/environmental-metadata') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = ENVMD - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class TopicId(NamedEntityId): - pass - - -class LocationId(NamedEntityId): - pass - - -class EnvironmentalMaterialId(NamedEntityId): - pass - - -class EnvironmentId(NamedEntityId): - pass - - -class MethodId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class Dataset(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ENVMD.Dataset - class_class_curie: ClassVar[str] = "envmd:Dataset" - class_name: ClassVar[str] = "Dataset" - class_model_uri: ClassVar[URIRef] = ENVMD.Dataset - - packageid: Optional[str] = None - topic: Optional[Union[Union[str, TopicId], List[Union[str, TopicId]]]] = empty_list() - location: Optional[Union[Union[str, LocationId], List[Union[str, LocationId]]]] = empty_list() - environmental_material: Optional[Union[Union[str, EnvironmentalMaterialId], List[Union[str, EnvironmentalMaterialId]]]] = empty_list() - environments: Optional[Union[Union[str, EnvironmentId], List[Union[str, EnvironmentId]]]] = empty_list() - methods: Optional[Union[Union[str, MethodId], List[Union[str, MethodId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.packageid is not None and not isinstance(self.packageid, str): - self.packageid = str(self.packageid) - - if not isinstance(self.topic, list): - self.topic = [self.topic] if self.topic is not None else [] - self.topic = [v if isinstance(v, TopicId) else TopicId(v) for v in self.topic] - - if not isinstance(self.location, list): - self.location = [self.location] if self.location is not None else [] - self.location = [v if isinstance(v, LocationId) else LocationId(v) for v in self.location] - - if not isinstance(self.environmental_material, list): - self.environmental_material = [self.environmental_material] if self.environmental_material is not None else [] - self.environmental_material = [v if isinstance(v, EnvironmentalMaterialId) else EnvironmentalMaterialId(v) for v in self.environmental_material] - - if not isinstance(self.environments, list): - self.environments = [self.environments] if self.environments is not None else [] - self.environments = [v if isinstance(v, EnvironmentId) else EnvironmentId(v) for v in self.environments] - - if not isinstance(self.methods, list): - self.methods = [self.methods] if self.methods is not None else [] - self.methods = [v if isinstance(v, MethodId) else MethodId(v) for v in self.methods] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = ENVMD.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = ENVMD.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Topic(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ENVMD.Topic - class_class_curie: ClassVar[str] = "envmd:Topic" - class_name: ClassVar[str] = "Topic" - class_model_uri: ClassVar[URIRef] = ENVMD.Topic - - id: Union[str, TopicId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, TopicId): - self.id = TopicId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Location(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ENVMD.Location - class_class_curie: ClassVar[str] = "envmd:Location" - class_name: ClassVar[str] = "Location" - class_model_uri: ClassVar[URIRef] = ENVMD.Location - - id: Union[str, LocationId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, LocationId): - self.id = LocationId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class EnvironmentalMaterial(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ENVMD.EnvironmentalMaterial - class_class_curie: ClassVar[str] = "envmd:EnvironmentalMaterial" - class_name: ClassVar[str] = "EnvironmentalMaterial" - class_model_uri: ClassVar[URIRef] = ENVMD.EnvironmentalMaterial - - id: Union[str, EnvironmentalMaterialId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EnvironmentalMaterialId): - self.id = EnvironmentalMaterialId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Environment(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ENVMD.Environment - class_class_curie: ClassVar[str] = "envmd:Environment" - class_name: ClassVar[str] = "Environment" - class_model_uri: ClassVar[URIRef] = ENVMD.Environment - - id: Union[str, EnvironmentId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EnvironmentId): - self.id = EnvironmentId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Method(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = ENVMD.Method - class_class_curie: ClassVar[str] = "envmd:Method" - class_name: ClassVar[str] = "Method" - class_model_uri: ClassVar[URIRef] = ENVMD.Method - - id: Union[str, MethodId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MethodId): - self.id = MethodId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = ENVMD.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = ENVMD.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = ENVMD.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = ENVMD.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = ENVMD.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = ENVMD.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.dataset__packageid = Slot(uri=ENVMD.packageid, name="dataset__packageid", curie=ENVMD.curie('packageid'), - model_uri=ENVMD.dataset__packageid, domain=None, range=Optional[str]) - -slots.dataset__topic = Slot(uri=ENVMD.topic, name="dataset__topic", curie=ENVMD.curie('topic'), - model_uri=ENVMD.dataset__topic, domain=None, range=Optional[Union[Union[str, TopicId], List[Union[str, TopicId]]]]) - -slots.dataset__location = Slot(uri=ENVMD.location, name="dataset__location", curie=ENVMD.curie('location'), - model_uri=ENVMD.dataset__location, domain=None, range=Optional[Union[Union[str, LocationId], List[Union[str, LocationId]]]]) - -slots.dataset__environmental_material = Slot(uri=ENVMD.environmental_material, name="dataset__environmental_material", curie=ENVMD.curie('environmental_material'), - model_uri=ENVMD.dataset__environmental_material, domain=None, range=Optional[Union[Union[str, EnvironmentalMaterialId], List[Union[str, EnvironmentalMaterialId]]]]) - -slots.dataset__environments = Slot(uri=ENVMD.environments, name="dataset__environments", curie=ENVMD.curie('environments'), - model_uri=ENVMD.dataset__environments, domain=None, range=Optional[Union[Union[str, EnvironmentId], List[Union[str, EnvironmentId]]]]) - -slots.dataset__methods = Slot(uri=ENVMD.methods, name="dataset__methods", curie=ENVMD.curie('methods'), - model_uri=ENVMD.dataset__methods, domain=None, range=Optional[Union[Union[str, MethodId], List[Union[str, MethodId]]]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=ENVMD.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=ENVMD.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=ENVMD.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=ENVMD.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=ENVMD.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=ENVMD.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=ENVMD.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=ENVMD.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=ENVMD.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=ENVMD.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=ENVMD.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=ENVMD.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=ENVMD.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=ENVMD.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=ENVMD.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=ENVMD.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=ENVMD.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=ENVMD.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=ENVMD.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=ENVMD.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=ENVMD.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=ENVMD.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=ENVMD.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=ENVMD.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=ENVMD.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/environmental_metadata/excel/environmental_metadata.xlsx b/projects/environmental_metadata/excel/environmental_metadata.xlsx deleted file mode 100644 index dabb228280148e7d8e58c3029391aa93e2c2f70e..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 10162 zcmeHtWl&sMw|3)Bg1fr}*WeI5Sdc*D7Tnz(g1ZDKxI=JAaCc~eJ0w7WU<od_!_>T) z@MXT5s#~|-KXbZHcXd^-r}uf*+WT2+?X4&a1&s*+0N??+YH%+lfE~#G;BVF7`!V=7 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ze-D~Gw0?Nd;}2T^z!#$GuhxGa`*>*n@F2ub^D*$>|K?c4Lx6`HVgCW}dkmg)V1VCl zi#<g7Yt{Cnh4km;>(>U3#^0daC#(M)g$FEmzd^a*diduk)yTg^x$mR@a};{i-=f?% zh5tE9E?C!o^F;R@&W9)u8+1R}B?O-h`VGo`yY3;%!|v2i6l3(?qTKhY9-=(#kNiZT z15b(HjOD&t@(|^(@$#eA{PXhlE5`aQ3hRB%{}AS3$@&w90_XQI_XX@jn1|KXPnb4v zF#qP6SbrP74@-mpz(7cYwF?aMvru?Af`^&iPtzX4U-G<%h7U8PpN17g{~7w9dDBDV vhwA#%xPj!}_;0lKA<jeP`H8bZ`db}Rl!XBw-U0wH!7niw06>HM$G86hTQ5mk diff --git a/projects/environmental_metadata/graphql/environmental_metadata.graphql b/projects/environmental_metadata/graphql/environmental_metadata.graphql deleted file mode 100644 index 40a51ae25..000000000 --- a/projects/environmental_metadata/graphql/environmental_metadata.graphql +++ /dev/null @@ -1,103 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type Dataset - { - packageid: String - topic: [Topic] - location: [Location] - environmentalMaterial: [EnvironmentalMaterial] - environments: [Environment] - methods: [Method] - } - -type Environment - { - id: String! - label: String - } - -type EnvironmentalMaterial - { - id: String! - label: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Location - { - id: String! - label: String - } - -type Method - { - id: String! - label: String - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -type Topic - { - id: String! - label: String - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/environmental_metadata/jsonld/environmental_metadata.context.jsonld b/projects/environmental_metadata/jsonld/environmental_metadata.context.jsonld deleted file mode 100644 index 68eaa9ed2..000000000 --- a/projects/environmental_metadata/jsonld/environmental_metadata.context.jsonld +++ /dev/null @@ -1,148 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:52:56", - "source": "environmental_metadata.yaml" - }, - "@context": { - "ENVO": "http://example.org/UNKNOWN/ENVO/", - "ENVTHES": "http://example.org/UNKNOWN/ENVTHES/", - "GAZ": "http://example.org/UNKNOWN/GAZ/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "envmd": { - "@id": "http://w3id.org/ontogpt/environmental-metadata", - "@prefix": true - }, - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/environmental-metadata", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "environmental_material": { - "@type": "@id" - }, - "environments": { - "@type": "@id" - }, - "location": { - "@type": "@id" - }, - "methods": { - "@type": "@id" - }, - "topic": { - "@type": "@id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/environmental_metadata/jsonld/environmental_metadata.jsonld b/projects/environmental_metadata/jsonld/environmental_metadata.jsonld deleted file mode 100644 index 7a10880a5..000000000 --- a/projects/environmental_metadata/jsonld/environmental_metadata.jsonld +++ /dev/null @@ -1,1314 +0,0 @@ -{ - "name": "environmental-metadata", - "description": "A template for categorizing Environmental Data Initiative data entries. See https://github.com/EDIorg/EDIorg-repository-index", - "title": "Environmental sample metadata", - "id": "http://w3id.org/ontogpt/environmental-metadata", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "envmd", - "prefix_reference": "http://w3id.org/ontogpt/environmental-metadata" - } - ], - "default_prefix": "envmd", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "dataset__packageid", - "annotations": [ - { - "tag": "prompt", - "value": "single unique identifier for the dataset", - "@type": "Annotation" - } - ], - "description": "The internal identifier for the dataset", - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "slot_uri": "http://w3id.org/ontogpt/environmental-metadatapackageid", - "alias": "packageid", - "owner": "Dataset", - "domain_of": [ - "Dataset" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "dataset__topic", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of scientific areas of study concerning the sample(s)", - "@type": "Annotation" - } - ], - "description": "the general scientific area of study concerning the sample(s)", - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "slot_uri": "http://w3id.org/ontogpt/environmental-metadatatopic", - "multivalued": true, - "alias": "topic", - "owner": "Dataset", - "domain_of": [ - "Dataset" - ], - "range": "Topic", - "@type": "SlotDefinition" - }, - { - "name": "dataset__location", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of geographic locations of sample isolations", - "@type": "Annotation" - } - ], - "description": "the geographic location where the sample was isolated", - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "slot_uri": "http://w3id.org/ontogpt/environmental-metadatalocation", - "multivalued": true, - "alias": "location", - "owner": "Dataset", - "domain_of": [ - "Dataset" - ], - "range": "Location", - "@type": "SlotDefinition" - }, - { - "name": "dataset__environmental_material", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental materials", - "@type": "Annotation" - } - ], - "description": "the environmental material that was sampled", - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "slot_uri": "http://w3id.org/ontogpt/environmental-metadataenvironmental_material", - "multivalued": true, - "alias": "environmental_material", - "owner": "Dataset", - "domain_of": [ - "Dataset" - ], - "range": "EnvironmentalMaterial", - "@type": "SlotDefinition" - }, - { - "name": "dataset__environments", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental contexts in which the study was conducted", - "@type": "Annotation" - } - ], - "description": "the environmental context in which the study was conducted", - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "slot_uri": "http://w3id.org/ontogpt/environmental-metadataenvironments", - "multivalued": true, - "alias": "environments", - "owner": "Dataset", - "domain_of": [ - "Dataset" - ], - "range": "Environment", - "@type": "SlotDefinition" - }, - { - "name": "dataset__methods", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of methods used in measuring sample variables", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "slot_uri": "http://w3id.org/ontogpt/environmental-metadatamethods", - "multivalued": true, - "alias": "methods", - "owner": "Dataset", - "domain_of": [ - "Dataset" - ], - "range": "Method", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Dataset", - "definition_uri": "http://w3id.org/ontogpt/environmental-metadataDataset", - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "slots": [ - "dataset__packageid", - "dataset__topic", - "dataset__location", - "dataset__environmental_material", - "dataset__environments", - "dataset__methods" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "packageid", - "annotations": [ - { - "tag": "prompt", - "value": "single unique identifier for the dataset", - "@type": "Annotation" - } - ], - "description": "The internal identifier for the dataset", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "topic", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of scientific areas of study concerning the sample(s)", - "@type": "Annotation" - } - ], - "description": "the general scientific area of study concerning the sample(s)", - "multivalued": true, - "range": "Topic", - "@type": "SlotDefinition" - }, - { - "name": "location", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of geographic locations of sample isolations", - "@type": "Annotation" - } - ], - "description": "the geographic location where the sample was isolated", - "multivalued": true, - "range": "Location", - "@type": "SlotDefinition" - }, - { - "name": "environmental_material", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental materials", - "@type": "Annotation" - } - ], - "description": "the environmental material that was sampled", - "multivalued": true, - "range": "EnvironmentalMaterial", - "@type": "SlotDefinition" - }, - { - "name": "environments", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental contexts in which the study was conducted", - "@type": "Annotation" - } - ], - "description": "the environmental context in which the study was conducted", - "multivalued": true, - "range": "Environment", - "@type": "SlotDefinition" - }, - { - "name": "methods", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of methods used in measuring sample variables", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "Method", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/environmental-metadataDataset", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Topic", - "id_prefixes": [ - "ENVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metadataTopic", - "annotations": [ - { - "tag": "annotators", - "value": "bioportal:ENVTHES", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metadataTopic", - "@type": "ClassDefinition" - }, - { - "name": "Location", - "id_prefixes": [ - "ENVO", - "GAZ" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metadataLocation", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:envo, bioportal:GAZ", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metadataLocation", - "@type": "ClassDefinition" - }, - { - "name": "EnvironmentalMaterial", - "id_prefixes": [ - "ENVO", - "ENVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:envo, bioportal:ENVTHES", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial", - "@type": "ClassDefinition" - }, - { - "name": "Environment", - "id_prefixes": [ - "ENVO", - "ENVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metadataEnvironment", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:envo, bioportal:ENVTHES", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metadataEnvironment", - "@type": "ClassDefinition" - }, - { - "name": "Method", - "id_prefixes": [ - "ENVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metadataMethod", - "annotations": [ - { - "tag": "annotators", - "value": "bioportal:ENVTHES", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-metadata", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metadataMethod", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "environmental_metadata.yaml", - "source_file_date": "2023-06-24T17:09:53", - "source_file_size": 2681, - "generation_date": "2023-08-07T10:52:57", - "@type": "SchemaDefinition", - "@context": [ - "projects/environmental_metadata/jsonld/environmental_metadata.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/environmental-metadata" - } - ] -} diff --git a/projects/environmental_metadata/jsonschema/environmental_metadata.schema.json b/projects/environmental_metadata/jsonschema/environmental_metadata.schema.json deleted file mode 100644 index ab7b0059c..000000000 --- a/projects/environmental_metadata/jsonschema/environmental_metadata.schema.json +++ /dev/null @@ -1,322 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "Dataset": { - "additionalProperties": false, - "description": "", - "properties": { - "environmental_material": { - "description": "the environmental material that was sampled", - "items": { - "type": "string" - }, - "type": "array" - }, - "environments": { - "description": "the environmental context in which the study was conducted", - "items": { - "type": "string" - }, - "type": "array" - }, - "location": { - "description": "the geographic location where the sample was isolated", - "items": { - "type": "string" - }, - "type": "array" - }, - "methods": { - "items": { - "type": "string" - }, - "type": "array" - }, - "packageid": { - "description": "The internal identifier for the dataset", - "type": "string" - }, - "topic": { - "description": "the general scientific area of study concerning the sample(s)", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "Dataset", - "type": "object" - }, - "Environment": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Environment", - "type": "object" - }, - "EnvironmentalMaterial": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "EnvironmentalMaterial", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Location": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Location", - "type": "object" - }, - "Method": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Method", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Topic": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Topic", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/environmental-metadata", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "environmental_material": { - "description": "the environmental material that was sampled", - "items": { - "type": "string" - }, - "type": "array" - }, - "environments": { - "description": "the environmental context in which the study was conducted", - "items": { - "type": "string" - }, - "type": "array" - }, - "location": { - "description": "the geographic location where the sample was isolated", - "items": { - "type": "string" - }, - "type": "array" - }, - "methods": { - "items": { - "type": "string" - }, - "type": "array" - }, - "packageid": { - "description": "The internal identifier for the dataset", - "type": "string" - }, - "topic": { - "description": "the general scientific area of study concerning the sample(s)", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "environmental-metadata", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/environmental_metadata/owl/environmental_metadata.owl.ttl b/projects/environmental_metadata/owl/environmental_metadata.owl.ttl deleted file mode 100644 index 9da750475..000000000 --- a/projects/environmental_metadata/owl/environmental_metadata.owl.ttl +++ /dev/null @@ -1,459 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix envmd: <http://w3id.org/ontogpt/environmental-metadata> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -envmd: a owl:Ontology ; - rdfs:label "environmental-metadata" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - envmd:Dataset ; - linkml:classes "{'Dataset': ClassDefinition(name='Dataset', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/environmental-metadataDataset', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-metadata', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['dataset__packageid', 'dataset__topic', 'dataset__location', 'dataset__environmental_material', 'dataset__environments', 'dataset__methods'], slot_usage={}, attributes={'packageid': SlotDefinition(name='packageid', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='single unique identifier for the dataset', extensions={}, annotations={})}, description='The internal identifier for the dataset', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=False, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'topic': SlotDefinition(name='topic', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of scientific areas of study concerning the sample(s)', extensions={}, annotations={})}, description='the general scientific area of study concerning the sample(s)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Topic', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of geographic locations of sample isolations', extensions={}, annotations={})}, description='the geographic location where the sample was isolated', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Location', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environmental_material': SlotDefinition(name='environmental_material', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental materials', extensions={}, annotations={})}, description='the environmental material that was sampled', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='EnvironmentalMaterial', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environments': SlotDefinition(name='environments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental contexts in which the study was conducted', extensions={}, annotations={})}, description='the environmental context in which the study was conducted', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Environment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'methods': SlotDefinition(name='methods', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of methods used in measuring sample variables', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Method', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='envmd:Dataset', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Topic': ClassDefinition(name='Topic', id_prefixes=['ENVTHES'], definition_uri='http://w3id.org/ontogpt/environmental-metadataTopic', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='bioportal:ENVTHES', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-metadata', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='envmd:Topic', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Location': ClassDefinition(name='Location', id_prefixes=['ENVO', 'GAZ'], definition_uri='http://w3id.org/ontogpt/environmental-metadataLocation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:GAZ', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-metadata', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='envmd:Location', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'EnvironmentalMaterial': ClassDefinition(name='EnvironmentalMaterial', id_prefixes=['ENVO', 'ENVTHES'], definition_uri='http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:ENVTHES', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-metadata', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='envmd:EnvironmentalMaterial', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Environment': ClassDefinition(name='Environment', id_prefixes=['ENVO', 'ENVTHES'], definition_uri='http://w3id.org/ontogpt/environmental-metadataEnvironment', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:ENVTHES', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-metadata', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='envmd:Environment', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Method': ClassDefinition(name='Method', id_prefixes=['ENVTHES'], definition_uri='http://w3id.org/ontogpt/environmental-metadataMethod', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='bioportal:ENVTHES', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-metadata', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='envmd:Method', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/environmental-metadata" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - envmd:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -envmd:Dataset a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Dataset" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom envmd:Location ; - owl:onProperty envmd:location ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty envmd:packageid ], - [ a owl:Restriction ; - owl:allValuesFrom envmd:Environment ; - owl:onProperty envmd:environments ], - [ a owl:Restriction ; - owl:allValuesFrom envmd:Method ; - owl:onProperty envmd:methods ], - [ a owl:Restriction ; - owl:allValuesFrom envmd:Topic ; - owl:onProperty envmd:topic ], - [ a owl:Restriction ; - owl:allValuesFrom envmd:EnvironmentalMaterial ; - owl:onProperty envmd:environmental_material ] ; - linkml:attributes "{'packageid': SlotDefinition(name='packageid', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='single unique identifier for the dataset', extensions={}, annotations={})}, description='The internal identifier for the dataset', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=False, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'topic': SlotDefinition(name='topic', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of scientific areas of study concerning the sample(s)', extensions={}, annotations={})}, description='the general scientific area of study concerning the sample(s)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Topic', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of geographic locations of sample isolations', extensions={}, annotations={})}, description='the geographic location where the sample was isolated', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Location', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environmental_material': SlotDefinition(name='environmental_material', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental materials', extensions={}, annotations={})}, description='the environmental material that was sampled', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='EnvironmentalMaterial', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environments': SlotDefinition(name='environments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental contexts in which the study was conducted', extensions={}, annotations={})}, description='the environmental context in which the study was conducted', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Environment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'methods': SlotDefinition(name='methods', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of methods used in measuring sample variables', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Method', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -envmd:environmental_material a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "environmental_material" ; - envmd:prompt "semicolon-separated list of environmental materials" ; - rdfs:range envmd:EnvironmentalMaterial ; - skos:definition "the environmental material that was sampled" . - -envmd:environments a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "environments" ; - envmd:prompt "semicolon-separated list of environmental contexts in which the study was conducted" ; - rdfs:range envmd:Environment ; - skos:definition "the environmental context in which the study was conducted" . - -envmd:location a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "location" ; - envmd:prompt "semicolon-separated list of geographic locations of sample isolations" ; - rdfs:range envmd:Location ; - skos:definition "the geographic location where the sample was isolated" . - -envmd:methods a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "methods" ; - envmd:prompt "semicolon-separated list of methods used in measuring sample variables" ; - rdfs:range envmd:Method . - -envmd:packageid a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "packageid" ; - envmd:prompt "single unique identifier for the dataset" ; - rdfs:range linkml:String ; - skos:definition "The internal identifier for the dataset" . - -envmd:topic a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "topic" ; - envmd:prompt "semicolon-separated list of scientific areas of study concerning the sample(s)" ; - rdfs:range envmd:Topic ; - skos:definition "the general scientific area of study concerning the sample(s)" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - envmd:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -envmd:Environment a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Environment" ; - envmd:annotators "sqlite:obo:envo, bioportal:ENVTHES" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -envmd:EnvironmentalMaterial a owl:Class, - linkml:ClassDefinition ; - rdfs:label "EnvironmentalMaterial" ; - envmd:annotators "sqlite:obo:envo, bioportal:ENVTHES" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -envmd:Location a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Location" ; - envmd:annotators "sqlite:obo:envo, bioportal:GAZ" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -envmd:Method a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Method" ; - envmd:annotators "bioportal:ENVTHES" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -envmd:Topic a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Topic" ; - envmd:annotators "bioportal:ENVTHES" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/environmental_metadata/prefixmap/environmental_metadata.yaml b/projects/environmental_metadata/prefixmap/environmental_metadata.yaml deleted file mode 100644 index 43f93149a..000000000 --- a/projects/environmental_metadata/prefixmap/environmental_metadata.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{ - "ENVO": "http://example.org/UNKNOWN/ENVO/", - "ENVTHES": "http://example.org/UNKNOWN/ENVTHES/", - "GAZ": "http://example.org/UNKNOWN/GAZ/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "envmd": "http://w3id.org/ontogpt/environmental-metadata", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/environmental_metadata/protobuf/environmental_metadata.proto b/projects/environmental_metadata/protobuf/environmental_metadata.proto deleted file mode 100644 index 5ce9c7df5..000000000 --- a/projects/environmental_metadata/protobuf/environmental_metadata.proto +++ /dev/null @@ -1,69 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message Dataset - { - string packageid = 0 - repeated topic topic = 0 - repeated location location = 0 - repeated environmentalMaterial environmentalMaterial = 0 - repeated environment environments = 0 - repeated method methods = 0 - } -message Environment - { - string id = 0 - string label = 0 - } -message EnvironmentalMaterial - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Location - { - string id = 0 - string label = 0 - } -message Method - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Topic - { - string id = 0 - string label = 0 - } diff --git a/projects/environmental_metadata/shacl/environmental_metadata.shacl.ttl b/projects/environmental_metadata/shacl/environmental_metadata.shacl.ttl deleted file mode 100644 index b45ae3a9b..000000000 --- a/projects/environmental_metadata/shacl/environmental_metadata.shacl.ttl +++ /dev/null @@ -1,267 +0,0 @@ -@prefix envmd: <http://w3id.org/ontogpt/environmental-metadata> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ], - [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -envmd:Dataset a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class envmd:EnvironmentalMaterial ; - sh:description "the environmental material that was sampled" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path envmd:environmental_material ], - [ sh:class envmd:Method ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path envmd:methods ], - [ sh:class envmd:Topic ; - sh:description "the general scientific area of study concerning the sample(s)" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path envmd:topic ], - [ sh:class envmd:Location ; - sh:description "the geographic location where the sample was isolated" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path envmd:location ], - [ sh:description "The internal identifier for the dataset" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path envmd:packageid ], - [ sh:class envmd:Environment ; - sh:description "the environmental context in which the study was conducted" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path envmd:environments ] ; - sh:targetClass envmd:Dataset . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -envmd:Environment a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass envmd:Environment . - -envmd:EnvironmentalMaterial a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass envmd:EnvironmentalMaterial . - -envmd:Location a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass envmd:Location . - -envmd:Method a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass envmd:Method . - -envmd:Topic a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass envmd:Topic . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/environmental_metadata/shex/environmental_metadata.shex b/projects/environmental_metadata/shex/environmental_metadata.shex deleted file mode 100644 index cd72663c0..000000000 --- a/projects/environmental_metadata/shex/environmental_metadata.shex +++ /dev/null @@ -1,192 +0,0 @@ -BASE <http://w3id.org/ontogpt/environmental-metadata/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -<http://w3id.org/ontogpt/environmental-metadataDataset> CLOSED { - ( $<http://w3id.org/ontogpt/environmental-metadataDataset_tes> ( <http://w3id.org/ontogpt/environmental-metadatapackageid> - @linkml:String ? ; - <http://w3id.org/ontogpt/environmental-metadatatopic> @<http://w3id.org/ontogpt/environmental-metadataTopic> * ; - <http://w3id.org/ontogpt/environmental-metadatalocation> @<http://w3id.org/ontogpt/environmental-metadataLocation> * ; - <http://w3id.org/ontogpt/environmental-metadataenvironmental_material> - @<http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial> * ; - <http://w3id.org/ontogpt/environmental-metadataenvironments> @<http://w3id.org/ontogpt/environmental-metadataEnvironment> - * ; - <http://w3id.org/ontogpt/environmental-metadatamethods> @<http://w3id.org/ontogpt/environmental-metadataMethod> * - ) ; - rdf:type [ <http://w3id.org/ontogpt/environmental-metadataDataset> ] ? - ) -} - -<http://w3id.org/ontogpt/environmental-metadataEnvironment> CLOSED { - ( $<http://w3id.org/ontogpt/environmental-metadataEnvironment_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/environmental-metadataEnvironment> ] - ) -} - -<http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial> CLOSED { - ( $<http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial> ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<http://w3id.org/ontogpt/environmental-metadataLocation> CLOSED { - ( $<http://w3id.org/ontogpt/environmental-metadataLocation_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/environmental-metadataLocation> ] - ) -} - -<http://w3id.org/ontogpt/environmental-metadataMethod> CLOSED { - ( $<http://w3id.org/ontogpt/environmental-metadataMethod_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/environmental-metadataMethod> ] - ) -} - -core:NamedEntity ( - @<http://w3id.org/ontogpt/environmental-metadataEnvironment> OR - @<http://w3id.org/ontogpt/environmental-metadataEnvironmentalMaterial> OR - @<http://w3id.org/ontogpt/environmental-metadataLocation> OR @<http://w3id.org/ontogpt/environmental-metadataMethod> OR - @core:RelationshipType OR @<http://w3id.org/ontogpt/environmental-metadataTopic> -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -<http://w3id.org/ontogpt/environmental-metadataTopic> CLOSED { - ( $<http://w3id.org/ontogpt/environmental-metadataTopic_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/environmental-metadataTopic> ] - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/environmental_metadata/sqlschema/environmental_metadata.sql b/projects/environmental_metadata/sqlschema/environmental_metadata.sql deleted file mode 100644 index db165bba3..000000000 --- a/projects/environmental_metadata/sqlschema/environmental_metadata.sql +++ /dev/null @@ -1,80 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Dataset" ( - packageid TEXT, - topic TEXT, - location TEXT, - environmental_material TEXT, - environments TEXT, - methods TEXT, - PRIMARY KEY (packageid, topic, location, environmental_material, environments, methods) -); - -CREATE TABLE "Environment" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "EnvironmentalMaterial" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Location" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Method" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Topic" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); diff --git a/projects/environmental_sample/docs/AnnotatorResult.md b/projects/environmental_sample/docs/AnnotatorResult.md deleted file mode 100644 index 47c39c704..000000000 --- a/projects/environmental_sample/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [sample:AnnotatorResult](http://w3id.org/ontogpt/environmental-sample/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/Any.md b/projects/environmental_sample/docs/Any.md deleted file mode 100644 index fa11e8c74..000000000 --- a/projects/environmental_sample/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [sample:Any](http://w3id.org/ontogpt/environmental-sample/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/environmental_sample/docs/CausalRelationship.md b/projects/environmental_sample/docs/CausalRelationship.md deleted file mode 100644 index 983312157..000000000 --- a/projects/environmental_sample/docs/CausalRelationship.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: CausalRelationship - - - - -URI: [sample:CausalRelationship](http://w3id.org/ontogpt/environmental-sample/CausalRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[CompoundExpression],[Variable]<effect%200..1-%20[CausalRelationship],[Variable]<cause%200..1-%20[CausalRelationship],[Study]++-%20causal_relationships%200..*>[CausalRelationship],[CompoundExpression]^-[CausalRelationship],[Study])](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[CompoundExpression],[Variable]<effect%200..1-%20[CausalRelationship],[Variable]<cause%200..1-%20[CausalRelationship],[Study]++-%20causal_relationships%200..*>[CausalRelationship],[CompoundExpression]^-[CausalRelationship],[Study]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞causal_relationships](study__causal_relationships.md)* <sub>0..\*</sub> **[CausalRelationship](CausalRelationship.md)** - -## Attributes - - -### Own - - * [➞cause](causalRelationship__cause.md) <sub>0..1</sub> - * Description: the variable that is the cause of the effect - * Range: [Variable](Variable.md) - * [➞effect](causalRelationship__effect.md) <sub>0..1</sub> - * Description: the things that is affected - * Range: [Variable](Variable.md) diff --git a/projects/environmental_sample/docs/CompoundExpression.md b/projects/environmental_sample/docs/CompoundExpression.md deleted file mode 100644 index 26b43451d..000000000 --- a/projects/environmental_sample/docs/CompoundExpression.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [sample:CompoundExpression](http://w3id.org/ontogpt/environmental-sample/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Measurement],[CompoundExpression]^-[Triple],[CompoundExpression]^-[Measurement],[CompoundExpression]^-[CausalRelationship],[CausalRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Measurement],[CompoundExpression]^-[Triple],[CompoundExpression]^-[Measurement],[CompoundExpression]^-[CausalRelationship],[CausalRelationship]) - -## Children - - * [CausalRelationship](CausalRelationship.md) - * [Measurement](Measurement.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/environmental_sample/docs/Environment.md b/projects/environmental_sample/docs/Environment.md deleted file mode 100644 index 424cc54eb..000000000 --- a/projects/environmental_sample/docs/Environment.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Environment - - - - -URI: [sample:Environment](http://w3id.org/ontogpt/environmental-sample/Environment) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20environments%200..*>[Environment|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Environment],[Study])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20environments%200..*>[Environment|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Environment],[Study]) - -## Identifier prefixes - - * ENVO - * ENVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞environments](study__environments.md)* <sub>0..\*</sub> **[Environment](Environment.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/EnvironmentalMaterial.md b/projects/environmental_sample/docs/EnvironmentalMaterial.md deleted file mode 100644 index 79a700713..000000000 --- a/projects/environmental_sample/docs/EnvironmentalMaterial.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: EnvironmentalMaterial - - - - -URI: [sample:EnvironmentalMaterial](http://w3id.org/ontogpt/environmental-sample/EnvironmentalMaterial) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20environmental_material%200..*>[EnvironmentalMaterial|id(i):string;label(i):string%20%3F],[NamedEntity]^-[EnvironmentalMaterial],[Study])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20environmental_material%200..*>[EnvironmentalMaterial|id(i):string;label(i):string%20%3F],[NamedEntity]^-[EnvironmentalMaterial],[Study]) - -## Identifier prefixes - - * ENVO - * ENVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞environmental_material](study__environmental_material.md)* <sub>0..\*</sub> **[EnvironmentalMaterial](EnvironmentalMaterial.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/ExtractionResult.md b/projects/environmental_sample/docs/ExtractionResult.md deleted file mode 100644 index 4fbd920ef..000000000 --- a/projects/environmental_sample/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [sample:ExtractionResult](http://w3id.org/ontogpt/environmental-sample/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/environmental_sample/docs/Location.md b/projects/environmental_sample/docs/Location.md deleted file mode 100644 index ee259f0c9..000000000 --- a/projects/environmental_sample/docs/Location.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: Location - - - - -URI: [sample:Location](http://w3id.org/ontogpt/environmental-sample/Location) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20location%200..*>[Location|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Location],[Study])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20location%200..*>[Location|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Location],[Study]) - -## Identifier prefixes - - * ENVO - * GAZ - * ENVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞location](study__location.md)* <sub>0..\*</sub> **[Location](Location.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/Measurement.md b/projects/environmental_sample/docs/Measurement.md deleted file mode 100644 index 47e7284cc..000000000 --- a/projects/environmental_sample/docs/Measurement.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Measurement - - - - -URI: [sample:Measurement](http://w3id.org/ontogpt/environmental-sample/Measurement) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[Unit]<unit%200..1-%20[Measurement|value:string%20%3F],[Study]++-%20measurements%200..*>[Measurement],[CompoundExpression]^-[Measurement],[Study],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[Unit]<unit%200..1-%20[Measurement|value:string%20%3F],[Study]++-%20measurements%200..*>[Measurement],[CompoundExpression]^-[Measurement],[Study],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞measurements](study__measurements.md)* <sub>0..\*</sub> **[Measurement](Measurement.md)** - -## Attributes - - -### Own - - * [➞value](measurement__value.md) <sub>0..1</sub> - * Description: the value of the measurement - * Range: [String](types/String.md) - * [➞unit](measurement__unit.md) <sub>0..1</sub> - * Description: the unit of the measurement - * Range: [Unit](Unit.md) diff --git a/projects/environmental_sample/docs/NamedEntity.md b/projects/environmental_sample/docs/NamedEntity.md deleted file mode 100644 index ac02541b8..000000000 --- a/projects/environmental_sample/docs/NamedEntity.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [sample:NamedEntity](http://w3id.org/ontogpt/environmental-sample/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[Unit],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Variable],[NamedEntity]^-[Unit],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Location],[NamedEntity]^-[EnvironmentalMaterial],[NamedEntity]^-[Environment],[Triple],[Location],[EnvironmentalMaterial],[Environment])](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[Unit],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Variable],[NamedEntity]^-[Unit],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Location],[NamedEntity]^-[EnvironmentalMaterial],[NamedEntity]^-[Environment],[Triple],[Location],[EnvironmentalMaterial],[Environment]) - -## Children - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - * [Variable](Variable.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/NullDataOptions.md b/projects/environmental_sample/docs/NullDataOptions.md deleted file mode 100644 index d8cfd2ea1..000000000 --- a/projects/environmental_sample/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [sample:NullDataOptions](http://w3id.org/ontogpt/environmental-sample/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/environmental_sample/docs/Publication.md b/projects/environmental_sample/docs/Publication.md deleted file mode 100644 index 03a8cab13..000000000 --- a/projects/environmental_sample/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [sample:Publication](http://w3id.org/ontogpt/environmental-sample/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/RelationshipType.md b/projects/environmental_sample/docs/RelationshipType.md deleted file mode 100644 index 833b5a697..000000000 --- a/projects/environmental_sample/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [sample:RelationshipType](http://w3id.org/ontogpt/environmental-sample/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/Study.md b/projects/environmental_sample/docs/Study.md deleted file mode 100644 index cdffa2f40..000000000 --- a/projects/environmental_sample/docs/Study.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Study - - - - -URI: [sample:Study](http://w3id.org/ontogpt/environmental-sample/Study) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[Measurement]<measurements%200..*-++[Study],[Variable]<variables%200..*-%20[Study],[CausalRelationship]<causal_relationships%200..*-++[Study],[Environment]<environments%200..*-%20[Study],[EnvironmentalMaterial]<environmental_material%200..*-%20[Study],[Location]<location%200..*-%20[Study],[Measurement],[Location],[EnvironmentalMaterial],[Environment],[CausalRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[Measurement]<measurements%200..*-++[Study],[Variable]<variables%200..*-%20[Study],[CausalRelationship]<causal_relationships%200..*-++[Study],[Environment]<environments%200..*-%20[Study],[EnvironmentalMaterial]<environmental_material%200..*-%20[Study],[Location]<location%200..*-%20[Study],[Measurement],[Location],[EnvironmentalMaterial],[Environment],[CausalRelationship]) - -## Attributes - - -### Own - - * [➞location](study__location.md) <sub>0..\*</sub> - * Description: the sites at which the study was conducted - * Range: [Location](Location.md) - * [➞environmental_material](study__environmental_material.md) <sub>0..\*</sub> - * Description: the environmental material that was sampled - * Range: [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [➞environments](study__environments.md) <sub>0..\*</sub> - * Range: [Environment](Environment.md) - * [➞causal_relationships](study__causal_relationships.md) <sub>0..\*</sub> - * Range: [CausalRelationship](CausalRelationship.md) - * [➞variables](study__variables.md) <sub>0..\*</sub> - * Range: [Variable](Variable.md) - * [➞measurements](study__measurements.md) <sub>0..\*</sub> - * Range: [Measurement](Measurement.md) diff --git a/projects/environmental_sample/docs/TextWithTriples.md b/projects/environmental_sample/docs/TextWithTriples.md deleted file mode 100644 index 966723bb6..000000000 --- a/projects/environmental_sample/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [sample:TextWithTriples](http://w3id.org/ontogpt/environmental-sample/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/environmental_sample/docs/Triple.md b/projects/environmental_sample/docs/Triple.md deleted file mode 100644 index 4d4252eaf..000000000 --- a/projects/environmental_sample/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [sample:Triple](http://w3id.org/ontogpt/environmental-sample/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/environmental_sample/docs/Unit.md b/projects/environmental_sample/docs/Unit.md deleted file mode 100644 index e52b832f4..000000000 --- a/projects/environmental_sample/docs/Unit.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Unit - - - - -URI: [sample:Unit](http://w3id.org/ontogpt/environmental-sample/Unit) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Measurement]-%20unit%200..1>[Unit|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Unit],[NamedEntity],[Measurement])](https://yuml.me/diagram/nofunky;dir:TB/class/[Measurement]-%20unit%200..1>[Unit|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Unit],[NamedEntity],[Measurement]) - -## Identifier prefixes - - * UO - * NCIT - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞unit](measurement__unit.md)* <sub>0..1</sub> **[Unit](Unit.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/Variable.md b/projects/environmental_sample/docs/Variable.md deleted file mode 100644 index 90bfc2919..000000000 --- a/projects/environmental_sample/docs/Variable.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Variable - - - - -URI: [sample:Variable](http://w3id.org/ontogpt/environmental-sample/Variable) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[CausalRelationship]-%20cause%200..1>[Variable|id(i):string;label(i):string%20%3F],[CausalRelationship]-%20effect%200..1>[Variable],[Study]-%20variables%200..*>[Variable],[NamedEntity]^-[Variable],[Study],[NamedEntity],[CausalRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[CausalRelationship]-%20cause%200..1>[Variable|id(i):string;label(i):string%20%3F],[CausalRelationship]-%20effect%200..1>[Variable],[Study]-%20variables%200..*>[Variable],[NamedEntity]^-[Variable],[Study],[NamedEntity],[CausalRelationship]) - -## Identifier prefixes - - * ENVO - * MIXS - * PATO - * ENVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞cause](causalRelationship__cause.md)* <sub>0..1</sub> **[Variable](Variable.md)** - * **None** *[➞effect](causalRelationship__effect.md)* <sub>0..1</sub> **[Variable](Variable.md)** - * **None** *[➞variables](study__variables.md)* <sub>0..\*</sub> **[Variable](Variable.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/environmental_sample/docs/annotatorResult__object_id.md b/projects/environmental_sample/docs/annotatorResult__object_id.md deleted file mode 100644 index 0c6c250bc..000000000 --- a/projects/environmental_sample/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [sample:annotatorResult__object_id](http://w3id.org/ontogpt/environmental-sample/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/environmental_sample/docs/annotatorResult__object_text.md b/projects/environmental_sample/docs/annotatorResult__object_text.md deleted file mode 100644 index 82aa42a0f..000000000 --- a/projects/environmental_sample/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [sample:annotatorResult__object_text](http://w3id.org/ontogpt/environmental-sample/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/environmental_sample/docs/annotatorResult__subject_text.md b/projects/environmental_sample/docs/annotatorResult__subject_text.md deleted file mode 100644 index caf48ada0..000000000 --- a/projects/environmental_sample/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [sample:annotatorResult__subject_text](http://w3id.org/ontogpt/environmental-sample/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/environmental_sample/docs/causalRelationship__cause.md b/projects/environmental_sample/docs/causalRelationship__cause.md deleted file mode 100644 index dd0594271..000000000 --- a/projects/environmental_sample/docs/causalRelationship__cause.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: cause - - -the variable that is the cause of the effect - -URI: [sample:causalRelationship__cause](http://w3id.org/ontogpt/environmental-sample/causalRelationship__cause) - - -## Domain and Range - -None → <sub>0..1</sub> [Variable](Variable.md) - -## Parents - - -## Children - - -## Used by - - * [CausalRelationship](CausalRelationship.md) diff --git a/projects/environmental_sample/docs/causalRelationship__effect.md b/projects/environmental_sample/docs/causalRelationship__effect.md deleted file mode 100644 index bfa059238..000000000 --- a/projects/environmental_sample/docs/causalRelationship__effect.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: effect - - -the things that is affected - -URI: [sample:causalRelationship__effect](http://w3id.org/ontogpt/environmental-sample/causalRelationship__effect) - - -## Domain and Range - -None → <sub>0..1</sub> [Variable](Variable.md) - -## Parents - - -## Children - - -## Used by - - * [CausalRelationship](CausalRelationship.md) diff --git a/projects/environmental_sample/docs/environmental_sample.md b/projects/environmental_sample/docs/environmental_sample.md deleted file mode 100644 index f40df4349..000000000 --- a/projects/environmental_sample/docs/environmental_sample.md +++ /dev/null @@ -1,121 +0,0 @@ - -# environmental-sample - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for Environmental Samples - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [CausalRelationship](CausalRelationship.md) - * [Measurement](Measurement.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - * [Variable](Variable.md) - * [Publication](Publication.md) - * [Study](Study.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞cause](causalRelationship__cause.md) - the variable that is the cause of the effect - * [➞effect](causalRelationship__effect.md) - the things that is affected - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞unit](measurement__unit.md) - the unit of the measurement - * [➞value](measurement__value.md) - the value of the measurement - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞causal_relationships](study__causal_relationships.md) - * [➞environmental_material](study__environmental_material.md) - the environmental material that was sampled - * [➞environments](study__environments.md) - * [➞location](study__location.md) - the sites at which the study was conducted - * [➞measurements](study__measurements.md) - * [➞variables](study__variables.md) - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/environmental_sample/docs/extractionResult__extracted_object.md b/projects/environmental_sample/docs/extractionResult__extracted_object.md deleted file mode 100644 index 19207749e..000000000 --- a/projects/environmental_sample/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [sample:extractionResult__extracted_object](http://w3id.org/ontogpt/environmental-sample/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_sample/docs/extractionResult__input_id.md b/projects/environmental_sample/docs/extractionResult__input_id.md deleted file mode 100644 index dd7b61fc6..000000000 --- a/projects/environmental_sample/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [sample:extractionResult__input_id](http://w3id.org/ontogpt/environmental-sample/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_sample/docs/extractionResult__input_text.md b/projects/environmental_sample/docs/extractionResult__input_text.md deleted file mode 100644 index 247ac72cd..000000000 --- a/projects/environmental_sample/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [sample:extractionResult__input_text](http://w3id.org/ontogpt/environmental-sample/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_sample/docs/extractionResult__input_title.md b/projects/environmental_sample/docs/extractionResult__input_title.md deleted file mode 100644 index 9fa9579bd..000000000 --- a/projects/environmental_sample/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [sample:extractionResult__input_title](http://w3id.org/ontogpt/environmental-sample/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_sample/docs/extractionResult__named_entities.md b/projects/environmental_sample/docs/extractionResult__named_entities.md deleted file mode 100644 index 727eae8e0..000000000 --- a/projects/environmental_sample/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [sample:extractionResult__named_entities](http://w3id.org/ontogpt/environmental-sample/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_sample/docs/extractionResult__prompt.md b/projects/environmental_sample/docs/extractionResult__prompt.md deleted file mode 100644 index 6b58c69e9..000000000 --- a/projects/environmental_sample/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [sample:extractionResult__prompt](http://w3id.org/ontogpt/environmental-sample/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_sample/docs/extractionResult__raw_completion_output.md b/projects/environmental_sample/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index d2ebc054e..000000000 --- a/projects/environmental_sample/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [sample:extractionResult__raw_completion_output](http://w3id.org/ontogpt/environmental-sample/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/environmental_sample/docs/measurement__unit.md b/projects/environmental_sample/docs/measurement__unit.md deleted file mode 100644 index 5b8c73c70..000000000 --- a/projects/environmental_sample/docs/measurement__unit.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: unit - - -the unit of the measurement - -URI: [sample:measurement__unit](http://w3id.org/ontogpt/environmental-sample/measurement__unit) - - -## Domain and Range - -None → <sub>0..1</sub> [Unit](Unit.md) - -## Parents - - -## Children - - -## Used by - - * [Measurement](Measurement.md) diff --git a/projects/environmental_sample/docs/measurement__value.md b/projects/environmental_sample/docs/measurement__value.md deleted file mode 100644 index 7409934f3..000000000 --- a/projects/environmental_sample/docs/measurement__value.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: value - - -the value of the measurement - -URI: [sample:measurement__value](http://w3id.org/ontogpt/environmental-sample/measurement__value) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Measurement](Measurement.md) diff --git a/projects/environmental_sample/docs/namedEntity__id.md b/projects/environmental_sample/docs/namedEntity__id.md deleted file mode 100644 index 8b066b213..000000000 --- a/projects/environmental_sample/docs/namedEntity__id.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [sample:namedEntity__id](http://w3id.org/ontogpt/environmental-sample/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - * [Variable](Variable.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/environmental_sample/docs/namedEntity__label.md b/projects/environmental_sample/docs/namedEntity__label.md deleted file mode 100644 index 746d61cb4..000000000 --- a/projects/environmental_sample/docs/namedEntity__label.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [sample:namedEntity__label](http://w3id.org/ontogpt/environmental-sample/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - * [Variable](Variable.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/environmental_sample/docs/publication__abstract.md b/projects/environmental_sample/docs/publication__abstract.md deleted file mode 100644 index b02cadb58..000000000 --- a/projects/environmental_sample/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [sample:publication__abstract](http://w3id.org/ontogpt/environmental-sample/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_sample/docs/publication__combined_text.md b/projects/environmental_sample/docs/publication__combined_text.md deleted file mode 100644 index 6c8e47f42..000000000 --- a/projects/environmental_sample/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [sample:publication__combined_text](http://w3id.org/ontogpt/environmental-sample/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_sample/docs/publication__full_text.md b/projects/environmental_sample/docs/publication__full_text.md deleted file mode 100644 index d844ec02c..000000000 --- a/projects/environmental_sample/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [sample:publication__full_text](http://w3id.org/ontogpt/environmental-sample/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_sample/docs/publication__id.md b/projects/environmental_sample/docs/publication__id.md deleted file mode 100644 index 5b8e23e69..000000000 --- a/projects/environmental_sample/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [sample:publication__id](http://w3id.org/ontogpt/environmental-sample/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_sample/docs/publication__title.md b/projects/environmental_sample/docs/publication__title.md deleted file mode 100644 index c031cc577..000000000 --- a/projects/environmental_sample/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [sample:publication__title](http://w3id.org/ontogpt/environmental-sample/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/environmental_sample/docs/study__causal_relationships.md b/projects/environmental_sample/docs/study__causal_relationships.md deleted file mode 100644 index 755de60e3..000000000 --- a/projects/environmental_sample/docs/study__causal_relationships.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: causal_relationships - - - - -URI: [sample:study__causal_relationships](http://w3id.org/ontogpt/environmental-sample/study__causal_relationships) - - -## Domain and Range - -None → <sub>0..\*</sub> [CausalRelationship](CausalRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/environmental_sample/docs/study__environmental_material.md b/projects/environmental_sample/docs/study__environmental_material.md deleted file mode 100644 index f654199dd..000000000 --- a/projects/environmental_sample/docs/study__environmental_material.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: environmental_material - - -the environmental material that was sampled - -URI: [sample:study__environmental_material](http://w3id.org/ontogpt/environmental-sample/study__environmental_material) - - -## Domain and Range - -None → <sub>0..\*</sub> [EnvironmentalMaterial](EnvironmentalMaterial.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/environmental_sample/docs/study__environments.md b/projects/environmental_sample/docs/study__environments.md deleted file mode 100644 index 3b10f1357..000000000 --- a/projects/environmental_sample/docs/study__environments.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: environments - - - - -URI: [sample:study__environments](http://w3id.org/ontogpt/environmental-sample/study__environments) - - -## Domain and Range - -None → <sub>0..\*</sub> [Environment](Environment.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/environmental_sample/docs/study__location.md b/projects/environmental_sample/docs/study__location.md deleted file mode 100644 index 90d1118fc..000000000 --- a/projects/environmental_sample/docs/study__location.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: location - - -the sites at which the study was conducted - -URI: [sample:study__location](http://w3id.org/ontogpt/environmental-sample/study__location) - - -## Domain and Range - -None → <sub>0..\*</sub> [Location](Location.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/environmental_sample/docs/study__measurements.md b/projects/environmental_sample/docs/study__measurements.md deleted file mode 100644 index 1905c2405..000000000 --- a/projects/environmental_sample/docs/study__measurements.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: measurements - - - - -URI: [sample:study__measurements](http://w3id.org/ontogpt/environmental-sample/study__measurements) - - -## Domain and Range - -None → <sub>0..\*</sub> [Measurement](Measurement.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/environmental_sample/docs/study__variables.md b/projects/environmental_sample/docs/study__variables.md deleted file mode 100644 index d0e9b4246..000000000 --- a/projects/environmental_sample/docs/study__variables.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: variables - - - - -URI: [sample:study__variables](http://w3id.org/ontogpt/environmental-sample/study__variables) - - -## Domain and Range - -None → <sub>0..\*</sub> [Variable](Variable.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/environmental_sample/docs/textWithTriples__publication.md b/projects/environmental_sample/docs/textWithTriples__publication.md deleted file mode 100644 index 5dc028075..000000000 --- a/projects/environmental_sample/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [sample:textWithTriples__publication](http://w3id.org/ontogpt/environmental-sample/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/environmental_sample/docs/textWithTriples__triples.md b/projects/environmental_sample/docs/textWithTriples__triples.md deleted file mode 100644 index ba158bb7e..000000000 --- a/projects/environmental_sample/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [sample:textWithTriples__triples](http://w3id.org/ontogpt/environmental-sample/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/environmental_sample/docs/triple__object.md b/projects/environmental_sample/docs/triple__object.md deleted file mode 100644 index 1b6e085ae..000000000 --- a/projects/environmental_sample/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [sample:triple__object](http://w3id.org/ontogpt/environmental-sample/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_sample/docs/triple__object_qualifier.md b/projects/environmental_sample/docs/triple__object_qualifier.md deleted file mode 100644 index 861af5475..000000000 --- a/projects/environmental_sample/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [sample:triple__object_qualifier](http://w3id.org/ontogpt/environmental-sample/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_sample/docs/triple__predicate.md b/projects/environmental_sample/docs/triple__predicate.md deleted file mode 100644 index 1c9dbb4f8..000000000 --- a/projects/environmental_sample/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [sample:triple__predicate](http://w3id.org/ontogpt/environmental-sample/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_sample/docs/triple__qualifier.md b/projects/environmental_sample/docs/triple__qualifier.md deleted file mode 100644 index 822e39281..000000000 --- a/projects/environmental_sample/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [sample:triple__qualifier](http://w3id.org/ontogpt/environmental-sample/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_sample/docs/triple__subject.md b/projects/environmental_sample/docs/triple__subject.md deleted file mode 100644 index f0761f24f..000000000 --- a/projects/environmental_sample/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [sample:triple__subject](http://w3id.org/ontogpt/environmental-sample/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_sample/docs/triple__subject_qualifier.md b/projects/environmental_sample/docs/triple__subject_qualifier.md deleted file mode 100644 index b8dcab9fe..000000000 --- a/projects/environmental_sample/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [sample:triple__subject_qualifier](http://w3id.org/ontogpt/environmental-sample/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/environmental_sample/docs/types/Boolean.md b/projects/environmental_sample/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/environmental_sample/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/environmental_sample/docs/types/Curie.md b/projects/environmental_sample/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/environmental_sample/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/environmental_sample/docs/types/Date.md b/projects/environmental_sample/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/environmental_sample/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/environmental_sample/docs/types/DateOrDatetime.md b/projects/environmental_sample/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/environmental_sample/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/environmental_sample/docs/types/Datetime.md b/projects/environmental_sample/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/environmental_sample/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/environmental_sample/docs/types/Decimal.md b/projects/environmental_sample/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/environmental_sample/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/environmental_sample/docs/types/Double.md b/projects/environmental_sample/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/environmental_sample/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/environmental_sample/docs/types/Float.md b/projects/environmental_sample/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/environmental_sample/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/environmental_sample/docs/types/Integer.md b/projects/environmental_sample/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/environmental_sample/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/environmental_sample/docs/types/Jsonpath.md b/projects/environmental_sample/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/environmental_sample/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/environmental_sample/docs/types/Jsonpointer.md b/projects/environmental_sample/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/environmental_sample/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/environmental_sample/docs/types/Ncname.md b/projects/environmental_sample/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/environmental_sample/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/environmental_sample/docs/types/Nodeidentifier.md b/projects/environmental_sample/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/environmental_sample/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/environmental_sample/docs/types/Objectidentifier.md b/projects/environmental_sample/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/environmental_sample/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/environmental_sample/docs/types/Sparqlpath.md b/projects/environmental_sample/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/environmental_sample/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/environmental_sample/docs/types/String.md b/projects/environmental_sample/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/environmental_sample/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/environmental_sample/docs/types/Time.md b/projects/environmental_sample/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/environmental_sample/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/environmental_sample/docs/types/Uri.md b/projects/environmental_sample/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/environmental_sample/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/environmental_sample/docs/types/Uriorcurie.md b/projects/environmental_sample/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/environmental_sample/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/environmental_sample/environmental_sample.py b/projects/environmental_sample/environmental_sample.py deleted file mode 100644 index 9fad60554..000000000 --- a/projects/environmental_sample/environmental_sample.py +++ /dev/null @@ -1,607 +0,0 @@ -# Auto generated from environmental_sample.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:53:18 -# Schema: environmental-sample -# -# id: http://w3id.org/ontogpt/environmental-sample -# description: A template for Environmental Samples -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -ENVO = CurieNamespace('ENVO', 'http://example.org/UNKNOWN/ENVO/') -ENVTHES = CurieNamespace('ENVTHES', 'http://example.org/UNKNOWN/ENVTHES/') -GAZ = CurieNamespace('GAZ', 'http://example.org/UNKNOWN/GAZ/') -MIXS = CurieNamespace('MIXS', 'http://example.org/UNKNOWN/MIXS/') -NCIT = CurieNamespace('NCIT', 'http://purl.obolibrary.org/obo/NCIT_') -PATO = CurieNamespace('PATO', 'http://example.org/UNKNOWN/PATO/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -UO = CurieNamespace('UO', 'http://example.org/UNKNOWN/UO/') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -SAMPLE = CurieNamespace('sample', 'http://w3id.org/ontogpt/environmental-sample/') -DEFAULT_ = SAMPLE - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class LocationId(NamedEntityId): - pass - - -class EnvironmentalMaterialId(NamedEntityId): - pass - - -class EnvironmentId(NamedEntityId): - pass - - -class VariableId(NamedEntityId): - pass - - -class UnitId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class Study(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SAMPLE.Study - class_class_curie: ClassVar[str] = "sample:Study" - class_name: ClassVar[str] = "Study" - class_model_uri: ClassVar[URIRef] = SAMPLE.Study - - location: Optional[Union[Union[str, LocationId], List[Union[str, LocationId]]]] = empty_list() - environmental_material: Optional[Union[Union[str, EnvironmentalMaterialId], List[Union[str, EnvironmentalMaterialId]]]] = empty_list() - environments: Optional[Union[Union[str, EnvironmentId], List[Union[str, EnvironmentId]]]] = empty_list() - causal_relationships: Optional[Union[Union[dict, "CausalRelationship"], List[Union[dict, "CausalRelationship"]]]] = empty_list() - variables: Optional[Union[Union[str, VariableId], List[Union[str, VariableId]]]] = empty_list() - measurements: Optional[Union[Union[dict, "Measurement"], List[Union[dict, "Measurement"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.location, list): - self.location = [self.location] if self.location is not None else [] - self.location = [v if isinstance(v, LocationId) else LocationId(v) for v in self.location] - - if not isinstance(self.environmental_material, list): - self.environmental_material = [self.environmental_material] if self.environmental_material is not None else [] - self.environmental_material = [v if isinstance(v, EnvironmentalMaterialId) else EnvironmentalMaterialId(v) for v in self.environmental_material] - - if not isinstance(self.environments, list): - self.environments = [self.environments] if self.environments is not None else [] - self.environments = [v if isinstance(v, EnvironmentId) else EnvironmentId(v) for v in self.environments] - - if not isinstance(self.causal_relationships, list): - self.causal_relationships = [self.causal_relationships] if self.causal_relationships is not None else [] - self.causal_relationships = [v if isinstance(v, CausalRelationship) else CausalRelationship(**as_dict(v)) for v in self.causal_relationships] - - if not isinstance(self.variables, list): - self.variables = [self.variables] if self.variables is not None else [] - self.variables = [v if isinstance(v, VariableId) else VariableId(v) for v in self.variables] - - if not isinstance(self.measurements, list): - self.measurements = [self.measurements] if self.measurements is not None else [] - self.measurements = [v if isinstance(v, Measurement) else Measurement(**as_dict(v)) for v in self.measurements] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = SAMPLE.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = SAMPLE.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Location(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SAMPLE.Location - class_class_curie: ClassVar[str] = "sample:Location" - class_name: ClassVar[str] = "Location" - class_model_uri: ClassVar[URIRef] = SAMPLE.Location - - id: Union[str, LocationId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, LocationId): - self.id = LocationId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class EnvironmentalMaterial(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SAMPLE.EnvironmentalMaterial - class_class_curie: ClassVar[str] = "sample:EnvironmentalMaterial" - class_name: ClassVar[str] = "EnvironmentalMaterial" - class_model_uri: ClassVar[URIRef] = SAMPLE.EnvironmentalMaterial - - id: Union[str, EnvironmentalMaterialId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EnvironmentalMaterialId): - self.id = EnvironmentalMaterialId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Environment(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SAMPLE.Environment - class_class_curie: ClassVar[str] = "sample:Environment" - class_name: ClassVar[str] = "Environment" - class_model_uri: ClassVar[URIRef] = SAMPLE.Environment - - id: Union[str, EnvironmentId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EnvironmentId): - self.id = EnvironmentId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Variable(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SAMPLE.Variable - class_class_curie: ClassVar[str] = "sample:Variable" - class_name: ClassVar[str] = "Variable" - class_model_uri: ClassVar[URIRef] = SAMPLE.Variable - - id: Union[str, VariableId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, VariableId): - self.id = VariableId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Unit(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SAMPLE.Unit - class_class_curie: ClassVar[str] = "sample:Unit" - class_name: ClassVar[str] = "Unit" - class_model_uri: ClassVar[URIRef] = SAMPLE.Unit - - id: Union[str, UnitId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, UnitId): - self.id = UnitId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = SAMPLE.CompoundExpression - - -@dataclass -class Measurement(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SAMPLE.Measurement - class_class_curie: ClassVar[str] = "sample:Measurement" - class_name: ClassVar[str] = "Measurement" - class_model_uri: ClassVar[URIRef] = SAMPLE.Measurement - - value: Optional[str] = None - unit: Optional[Union[str, UnitId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.value is not None and not isinstance(self.value, str): - self.value = str(self.value) - - if self.unit is not None and not isinstance(self.unit, UnitId): - self.unit = UnitId(self.unit) - - super().__post_init__(**kwargs) - - -@dataclass -class CausalRelationship(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = SAMPLE.CausalRelationship - class_class_curie: ClassVar[str] = "sample:CausalRelationship" - class_name: ClassVar[str] = "CausalRelationship" - class_model_uri: ClassVar[URIRef] = SAMPLE.CausalRelationship - - cause: Optional[Union[str, VariableId]] = None - effect: Optional[Union[str, VariableId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.cause is not None and not isinstance(self.cause, VariableId): - self.cause = VariableId(self.cause) - - if self.effect is not None and not isinstance(self.effect, VariableId): - self.effect = VariableId(self.effect) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = SAMPLE.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = SAMPLE.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = SAMPLE.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = SAMPLE.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = SAMPLE.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.study__location = Slot(uri=SAMPLE.location, name="study__location", curie=SAMPLE.curie('location'), - model_uri=SAMPLE.study__location, domain=None, range=Optional[Union[Union[str, LocationId], List[Union[str, LocationId]]]]) - -slots.study__environmental_material = Slot(uri=SAMPLE.environmental_material, name="study__environmental_material", curie=SAMPLE.curie('environmental_material'), - model_uri=SAMPLE.study__environmental_material, domain=None, range=Optional[Union[Union[str, EnvironmentalMaterialId], List[Union[str, EnvironmentalMaterialId]]]]) - -slots.study__environments = Slot(uri=SAMPLE.environments, name="study__environments", curie=SAMPLE.curie('environments'), - model_uri=SAMPLE.study__environments, domain=None, range=Optional[Union[Union[str, EnvironmentId], List[Union[str, EnvironmentId]]]]) - -slots.study__causal_relationships = Slot(uri=SAMPLE.causal_relationships, name="study__causal_relationships", curie=SAMPLE.curie('causal_relationships'), - model_uri=SAMPLE.study__causal_relationships, domain=None, range=Optional[Union[Union[dict, CausalRelationship], List[Union[dict, CausalRelationship]]]]) - -slots.study__variables = Slot(uri=SAMPLE.variables, name="study__variables", curie=SAMPLE.curie('variables'), - model_uri=SAMPLE.study__variables, domain=None, range=Optional[Union[Union[str, VariableId], List[Union[str, VariableId]]]]) - -slots.study__measurements = Slot(uri=SAMPLE.measurements, name="study__measurements", curie=SAMPLE.curie('measurements'), - model_uri=SAMPLE.study__measurements, domain=None, range=Optional[Union[Union[dict, Measurement], List[Union[dict, Measurement]]]]) - -slots.measurement__value = Slot(uri=SAMPLE.value, name="measurement__value", curie=SAMPLE.curie('value'), - model_uri=SAMPLE.measurement__value, domain=None, range=Optional[str]) - -slots.measurement__unit = Slot(uri=SAMPLE.unit, name="measurement__unit", curie=SAMPLE.curie('unit'), - model_uri=SAMPLE.measurement__unit, domain=None, range=Optional[Union[str, UnitId]]) - -slots.causalRelationship__cause = Slot(uri=SAMPLE.cause, name="causalRelationship__cause", curie=SAMPLE.curie('cause'), - model_uri=SAMPLE.causalRelationship__cause, domain=None, range=Optional[Union[str, VariableId]]) - -slots.causalRelationship__effect = Slot(uri=SAMPLE.effect, name="causalRelationship__effect", curie=SAMPLE.curie('effect'), - model_uri=SAMPLE.causalRelationship__effect, domain=None, range=Optional[Union[str, VariableId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=SAMPLE.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=SAMPLE.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=SAMPLE.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=SAMPLE.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=SAMPLE.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=SAMPLE.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=SAMPLE.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=SAMPLE.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=SAMPLE.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=SAMPLE.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=SAMPLE.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=SAMPLE.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=SAMPLE.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=SAMPLE.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=SAMPLE.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=SAMPLE.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=SAMPLE.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=SAMPLE.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=SAMPLE.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=SAMPLE.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=SAMPLE.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=SAMPLE.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=SAMPLE.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=SAMPLE.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=SAMPLE.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git 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a/projects/environmental_sample/graphql/environmental_sample.graphql +++ /dev/null @@ -1,115 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type CausalRelationship - { - cause: Variable - effect: Variable - } - -interface CompoundExpression - { - } - -type Environment - { - id: String! - label: String - } - -type EnvironmentalMaterial - { - id: String! - label: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Location - { - id: String! - label: String - } - -type Measurement - { - value: String - unit: Unit - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type Study - { - location: [Location] - environmentalMaterial: [EnvironmentalMaterial] - environments: [Environment] - causalRelationships: [CausalRelationship] - variables: [Variable] - measurements: [Measurement] - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - -type Unit - { - id: String! - label: String - } - -type Variable - { - id: String! - label: String - } - diff --git a/projects/environmental_sample/jsonld/environmental_sample.context.jsonld b/projects/environmental_sample/jsonld/environmental_sample.context.jsonld deleted file mode 100644 index e8fea7e3d..000000000 --- a/projects/environmental_sample/jsonld/environmental_sample.context.jsonld +++ /dev/null @@ -1,164 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:53:09", - "source": "environmental_sample.yaml" - }, - "@context": { - "ENVO": "http://example.org/UNKNOWN/ENVO/", - "ENVTHES": "http://example.org/UNKNOWN/ENVTHES/", - "GAZ": "http://example.org/UNKNOWN/GAZ/", - "MIXS": "http://example.org/UNKNOWN/MIXS/", - "NCIT": { - "@id": "http://purl.obolibrary.org/obo/NCIT_", - "@prefix": true - }, - "PATO": "http://example.org/UNKNOWN/PATO/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "UO": "http://example.org/UNKNOWN/UO/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "sample": "http://w3id.org/ontogpt/environmental-sample/", - "@vocab": "http://w3id.org/ontogpt/environmental-sample/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "cause": { - "@type": "@id" - }, - "effect": { - "@type": "@id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "unit": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "causal_relationships": { - "@type": "@id" - }, - "environmental_material": { - "@type": "@id" - }, - "environments": { - "@type": "@id" - }, - "location": { - "@type": "@id" - }, - "measurements": { - "@type": "@id" - }, - "variables": { - "@type": "@id" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/environmental_sample/jsonld/environmental_sample.jsonld b/projects/environmental_sample/jsonld/environmental_sample.jsonld deleted file mode 100644 index a1c9df94a..000000000 --- a/projects/environmental_sample/jsonld/environmental_sample.jsonld +++ /dev/null @@ -1,1422 +0,0 @@ -{ - "name": "environmental-sample", - "description": "A template for Environmental Samples", - "title": "Environmental Sample Template", - "id": "http://w3id.org/ontogpt/environmental-sample", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "sample", - "prefix_reference": "http://w3id.org/ontogpt/environmental-sample/" - } - ], - "default_prefix": "sample", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "study__location", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of sites at which the study was conducted. give specific place names. if you cannot find a specific place name leave the field as empty.", - "@type": "Annotation" - } - ], - "description": "the sites at which the study was conducted", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/location", - "multivalued": true, - "alias": "location", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Location", - "@type": "SlotDefinition" - }, - { - "name": "study__environmental_material", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental materials", - "@type": "Annotation" - } - ], - "description": "the environmental material that was sampled", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/environmental_material", - "multivalued": true, - "alias": "environmental_material", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "EnvironmentalMaterial", - "@type": "SlotDefinition" - }, - { - "name": "study__environments", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environment terms for the location in which the study was conducted", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/environments", - "multivalued": true, - "alias": "environments", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Environment", - "@type": "SlotDefinition" - }, - { - "name": "study__causal_relationships", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/causal_relationships", - "multivalued": true, - "alias": "causal_relationships", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "CausalRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "study__variables", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of study variables", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/variables", - "multivalued": true, - "alias": "variables", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Variable", - "@type": "SlotDefinition" - }, - { - "name": "study__measurements", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of value-measurement pairs", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/measurements", - "multivalued": true, - "alias": "measurements", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Measurement", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "measurement__value", - "description": "the value of the measurement", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/value", - "alias": "value", - "owner": "Measurement", - "domain_of": [ - "Measurement" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "measurement__unit", - "description": "the unit of the measurement", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/unit", - "alias": "unit", - "owner": "Measurement", - "domain_of": [ - "Measurement" - ], - "range": "Unit", - "@type": "SlotDefinition" - }, - { - "name": "causalRelationship__cause", - "description": "the variable that is the cause of the effect", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/cause", - "alias": "cause", - "owner": "CausalRelationship", - "domain_of": [ - "CausalRelationship" - ], - "range": "Variable", - "@type": "SlotDefinition" - }, - { - "name": "causalRelationship__effect", - "description": "the things that is affected", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slot_uri": "http://w3id.org/ontogpt/environmental-sample/effect", - "alias": "effect", - "owner": "CausalRelationship", - "domain_of": [ - "CausalRelationship" - ], - "range": "Variable", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Study", - "definition_uri": "http://w3id.org/ontogpt/environmental-sample/Study", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "slots": [ - "study__location", - "study__environmental_material", - "study__environments", - "study__causal_relationships", - "study__variables", - "study__measurements" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "location", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of sites at which the study was conducted. give specific place names. if you cannot find a specific place name leave the field as empty.", - "@type": "Annotation" - } - ], - "description": "the sites at which the study was conducted", - "multivalued": true, - "range": "Location", - "@type": "SlotDefinition" - }, - { - "name": "environmental_material", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental materials", - "@type": "Annotation" - } - ], - "description": "the environmental material that was sampled", - "multivalued": true, - "range": "EnvironmentalMaterial", - "@type": "SlotDefinition" - }, - { - "name": "environments", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environment terms for the location in which the study was conducted", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "Environment", - "@type": "SlotDefinition" - }, - { - "name": "causal_relationships", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "CausalRelationship", - "@type": "SlotDefinition" - }, - { - "name": "variables", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of study variables", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "Variable", - "@type": "SlotDefinition" - }, - { - "name": "measurements", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of value-measurement pairs", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "Measurement", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/environmental-sample/Study", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Location", - "id_prefixes": [ - "ENVO", - "GAZ", - "ENVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-sample/Location", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:envo, bioportal:gaz, bioportal:envthes", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-sample/Location", - "@type": "ClassDefinition" - }, - { - "name": "EnvironmentalMaterial", - "id_prefixes": [ - "ENVO", - "ENVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-sample/EnvironmentalMaterial", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:envo, bioportal:envthes", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-sample/EnvironmentalMaterial", - "@type": "ClassDefinition" - }, - { - "name": "Environment", - "id_prefixes": [ - "ENVO", - "ENVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-sample/Environment", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:envo, bioportal:envthes", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-sample/Environment", - "@type": "ClassDefinition" - }, - { - "name": "Variable", - "id_prefixes": [ - "ENVO", - "MIXS", - "PATO", - "ENVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-sample/Variable", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:envo, bioportal:bero, bioportal:envthes", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-sample/Variable", - "@type": "ClassDefinition" - }, - { - "name": "Unit", - "id_prefixes": [ - "UO", - "NCIT" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-sample/Unit", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:uo, bioportal:ncit", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-sample/Unit", - "@type": "ClassDefinition" - }, - { - "name": "Measurement", - "definition_uri": "http://w3id.org/ontogpt/environmental-sample/Measurement", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "is_a": "CompoundExpression", - "slots": [ - "measurement__value", - "measurement__unit" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "value", - "description": "the value of the measurement", - "@type": "SlotDefinition" - }, - { - "name": "unit", - "description": "the unit of the measurement", - "range": "Unit", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/environmental-sample/Measurement", - "@type": "ClassDefinition" - }, - { - "name": "CausalRelationship", - "definition_uri": "http://w3id.org/ontogpt/environmental-sample/CausalRelationship", - "from_schema": "http://w3id.org/ontogpt/environmental-sample", - "is_a": "CompoundExpression", - "slots": [ - "causalRelationship__cause", - "causalRelationship__effect" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "cause", - "description": "the variable that is the cause of the effect", - "range": "Variable", - "@type": "SlotDefinition" - }, - { - "name": "effect", - "description": "the things that is affected", - "range": "Variable", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/environmental-sample/CausalRelationship", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "environmental_sample.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 3147, - "generation_date": "2023-08-07T10:53:10", - "@type": "SchemaDefinition", - "@context": [ - "projects/environmental_sample/jsonld/environmental_sample.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/environmental-sample/" - } - ] -} diff --git a/projects/environmental_sample/jsonschema/environmental_sample.schema.json b/projects/environmental_sample/jsonschema/environmental_sample.schema.json deleted file mode 100644 index 551239e45..000000000 --- a/projects/environmental_sample/jsonschema/environmental_sample.schema.json +++ /dev/null @@ -1,354 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "CausalRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "cause": { - "description": "the variable that is the cause of the effect", - "type": "string" - }, - "effect": { - "description": "the things that is affected", - "type": "string" - } - }, - "title": "CausalRelationship", - "type": "object" - }, - "Environment": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Environment", - "type": "object" - }, - "EnvironmentalMaterial": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "EnvironmentalMaterial", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Location": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Location", - "type": "object" - }, - "Measurement": { - "additionalProperties": false, - "description": "", - "properties": { - "unit": { - "description": "the unit of the measurement", - "type": "string" - }, - "value": { - "description": "the value of the measurement", - "type": "string" - } - }, - "title": "Measurement", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "Study": { - "additionalProperties": false, - "description": "", - "properties": { - "causal_relationships": { - "items": { - "$ref": "#/$defs/CausalRelationship" - }, - "type": "array" - }, - "environmental_material": { - "description": "the environmental material that was sampled", - "items": { - "type": "string" - }, - "type": "array" - }, - "environments": { - "items": { - "type": "string" - }, - "type": "array" - }, - "location": { - "description": "the sites at which the study was conducted", - "items": { - "type": "string" - }, - "type": "array" - }, - "measurements": { - "items": { - "$ref": "#/$defs/Measurement" - }, - "type": "array" - }, - "variables": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "Study", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Unit": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Unit", - "type": "object" - }, - "Variable": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Variable", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/environmental-sample", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "causal_relationships": { - "items": { - "$ref": "#/$defs/CausalRelationship" - }, - "type": "array" - }, - "environmental_material": { - "description": "the environmental material that was sampled", - "items": { - "type": "string" - }, - "type": "array" - }, - "environments": { - "items": { - "type": "string" - }, - "type": "array" - }, - "location": { - "description": "the sites at which the study was conducted", - "items": { - "type": "string" - }, - "type": "array" - }, - "measurements": { - "items": { - "$ref": "#/$defs/Measurement" - }, - "type": "array" - }, - "variables": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "environmental-sample", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/environmental_sample/owl/environmental_sample.owl.ttl b/projects/environmental_sample/owl/environmental_sample.owl.ttl deleted file mode 100644 index 11e703611..000000000 --- a/projects/environmental_sample/owl/environmental_sample.owl.ttl +++ /dev/null @@ -1,509 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix sample: <http://w3id.org/ontogpt/environmental-sample/> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/environmental-sample> a owl:Ontology ; - rdfs:label "environmental-sample" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - sample:Study ; - linkml:classes "{'Study': ClassDefinition(name='Study', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/environmental-sample/Study', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-sample', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['study__location', 'study__environmental_material', 'study__environments', 'study__causal_relationships', 'study__variables', 'study__measurements'], slot_usage={}, attributes={'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of sites at which the study was conducted. give specific place names. if you cannot find a specific place name leave the field as empty.', extensions={}, annotations={})}, description='the sites at which the study was conducted', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Location', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environmental_material': SlotDefinition(name='environmental_material', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental materials', extensions={}, annotations={})}, description='the environmental material that was sampled', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='EnvironmentalMaterial', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environments': SlotDefinition(name='environments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environment terms for the location in which the study was conducted', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Environment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'causal_relationships': SlotDefinition(name='causal_relationships', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CausalRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'variables': SlotDefinition(name='variables', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of study variables', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'measurements': SlotDefinition(name='measurements', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of value-measurement pairs', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Measurement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='sample:Study', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Location': ClassDefinition(name='Location', id_prefixes=['ENVO', 'GAZ', 'ENVTHES'], definition_uri='http://w3id.org/ontogpt/environmental-sample/Location', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:gaz, bioportal:envthes', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-sample', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='sample:Location', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'EnvironmentalMaterial': ClassDefinition(name='EnvironmentalMaterial', id_prefixes=['ENVO', 'ENVTHES'], definition_uri='http://w3id.org/ontogpt/environmental-sample/EnvironmentalMaterial', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:envthes', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-sample', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='sample:EnvironmentalMaterial', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Environment': ClassDefinition(name='Environment', id_prefixes=['ENVO', 'ENVTHES'], definition_uri='http://w3id.org/ontogpt/environmental-sample/Environment', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:envthes', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-sample', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='sample:Environment', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Variable': ClassDefinition(name='Variable', id_prefixes=['ENVO', 'MIXS', 'PATO', 'ENVTHES'], definition_uri='http://w3id.org/ontogpt/environmental-sample/Variable', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:bero, bioportal:envthes', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-sample', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='sample:Variable', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Unit': ClassDefinition(name='Unit', id_prefixes=['UO', 'NCIT'], definition_uri='http://w3id.org/ontogpt/environmental-sample/Unit', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:uo, bioportal:ncit', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-sample', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='sample:Unit', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Measurement': ClassDefinition(name='Measurement', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/environmental-sample/Measurement', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-sample', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['measurement__value', 'measurement__unit'], slot_usage={}, attributes={'value': SlotDefinition(name='value', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the value of the measurement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'unit': SlotDefinition(name='unit', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the unit of the measurement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Unit', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='sample:Measurement', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CausalRelationship': ClassDefinition(name='CausalRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/environmental-sample/CausalRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/environmental-sample', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['causalRelationship__cause', 'causalRelationship__effect'], slot_usage={}, attributes={'cause': SlotDefinition(name='cause', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the variable that is the cause of the effect', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'effect': SlotDefinition(name='effect', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the things that is affected', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='sample:CausalRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/environmental-sample" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - sample:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -sample:Study a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Study" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom sample:Variable ; - owl:onProperty sample:variables ], - [ a owl:Restriction ; - owl:allValuesFrom sample:Measurement ; - owl:onProperty sample:measurements ], - [ a owl:Restriction ; - owl:allValuesFrom sample:Environment ; - owl:onProperty sample:environments ], - [ a owl:Restriction ; - owl:allValuesFrom sample:CausalRelationship ; - owl:onProperty sample:causal_relationships ], - [ a owl:Restriction ; - owl:allValuesFrom sample:Location ; - owl:onProperty sample:location ], - [ a owl:Restriction ; - owl:allValuesFrom sample:EnvironmentalMaterial ; - owl:onProperty sample:environmental_material ] ; - linkml:attributes "{'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of sites at which the study was conducted. give specific place names. if you cannot find a specific place name leave the field as empty.', extensions={}, annotations={})}, description='the sites at which the study was conducted', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Location', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environmental_material': SlotDefinition(name='environmental_material', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental materials', extensions={}, annotations={})}, description='the environmental material that was sampled', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='EnvironmentalMaterial', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environments': SlotDefinition(name='environments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environment terms for the location in which the study was conducted', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Environment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'causal_relationships': SlotDefinition(name='causal_relationships', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CausalRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'variables': SlotDefinition(name='variables', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of study variables', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'measurements': SlotDefinition(name='measurements', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of value-measurement pairs', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Measurement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -sample:causal_relationships a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "causal_relationships" ; - sample:prompt "semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth" ; - rdfs:range sample:CausalRelationship . - -sample:cause a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "cause" ; - rdfs:range sample:Variable ; - skos:definition "the variable that is the cause of the effect" . - -sample:effect a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "effect" ; - rdfs:range sample:Variable ; - skos:definition "the things that is affected" . - -sample:environmental_material a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "environmental_material" ; - sample:prompt "semicolon-separated list of environmental materials" ; - rdfs:range sample:EnvironmentalMaterial ; - skos:definition "the environmental material that was sampled" . - -sample:environments a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "environments" ; - sample:prompt "semicolon-separated list of environment terms for the location in which the study was conducted" ; - rdfs:range sample:Environment . - -sample:location a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "location" ; - sample:prompt "semicolon-separated list of sites at which the study was conducted. give specific place names. if you cannot find a specific place name leave the field as empty." ; - rdfs:range sample:Location ; - skos:definition "the sites at which the study was conducted" . - -sample:measurements a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "measurements" ; - sample:prompt "semicolon-separated list of value-measurement pairs" ; - rdfs:range sample:Measurement . - -sample:unit a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "unit" ; - rdfs:range sample:Unit ; - skos:definition "the unit of the measurement" . - -sample:value a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "value" ; - rdfs:range linkml:String ; - skos:definition "the value of the measurement" . - -sample:variables a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "variables" ; - sample:prompt "semicolon-separated list of study variables" ; - rdfs:range sample:Variable . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - sample:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -sample:CausalRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CausalRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass sample:Variable ; - owl:onProperty sample:effect ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass sample:Variable ; - owl:onProperty sample:cause ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'cause': SlotDefinition(name='cause', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the variable that is the cause of the effect', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'effect': SlotDefinition(name='effect', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the things that is affected', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -sample:Environment a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Environment" ; - sample:annotators "sqlite:obo:envo, bioportal:envthes" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -sample:EnvironmentalMaterial a owl:Class, - linkml:ClassDefinition ; - rdfs:label "EnvironmentalMaterial" ; - sample:annotators "sqlite:obo:envo, bioportal:envthes" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -sample:Location a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Location" ; - sample:annotators "sqlite:obo:envo, bioportal:gaz, bioportal:envthes" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -sample:Measurement a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Measurement" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty sample:value ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass sample:Unit ; - owl:onProperty sample:unit ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'value': SlotDefinition(name='value', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the value of the measurement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'unit': SlotDefinition(name='unit', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the unit of the measurement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Unit', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -sample:Unit a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Unit" ; - sample:annotators "sqlite:obo:uo, bioportal:ncit" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -sample:Variable a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Variable" ; - sample:annotators "sqlite:obo:envo, bioportal:bero, bioportal:envthes" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/environmental_sample/prefixmap/environmental_sample.yaml b/projects/environmental_sample/prefixmap/environmental_sample.yaml deleted file mode 100644 index c6e700268..000000000 --- a/projects/environmental_sample/prefixmap/environmental_sample.yaml +++ /dev/null @@ -1,42 +0,0 @@ -{ - "ENVO": "http://example.org/UNKNOWN/ENVO/", - "ENVTHES": "http://example.org/UNKNOWN/ENVTHES/", - "GAZ": "http://example.org/UNKNOWN/GAZ/", - "MIXS": "http://example.org/UNKNOWN/MIXS/", - "NCIT": "http://purl.obolibrary.org/obo/NCIT_", - "PATO": "http://example.org/UNKNOWN/PATO/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "UO": "http://example.org/UNKNOWN/UO/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "sample": "http://w3id.org/ontogpt/environmental-sample/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/environmental_sample/protobuf/environmental_sample.proto b/projects/environmental_sample/protobuf/environmental_sample.proto deleted file mode 100644 index 195a6f5e5..000000000 --- a/projects/environmental_sample/protobuf/environmental_sample.proto +++ /dev/null @@ -1,79 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message CausalRelationship - { - variable cause = 0 - variable effect = 0 - } -message Environment - { - string id = 0 - string label = 0 - } -message EnvironmentalMaterial - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Location - { - string id = 0 - string label = 0 - } -message Measurement - { - string value = 0 - unit unit = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message Study - { - repeated location location = 0 - repeated environmentalMaterial environmentalMaterial = 0 - repeated environment environments = 0 - repeated causalRelationship causalRelationships = 0 - repeated variable variables = 0 - repeated measurement measurements = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Unit - { - string id = 0 - string label = 0 - } -message Variable - { - string id = 0 - string label = 0 - } diff --git a/projects/environmental_sample/shacl/environmental_sample.shacl.ttl b/projects/environmental_sample/shacl/environmental_sample.shacl.ttl deleted file mode 100644 index f0d0f8b35..000000000 --- a/projects/environmental_sample/shacl/environmental_sample.shacl.ttl +++ /dev/null @@ -1,297 +0,0 @@ -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sample: <http://w3id.org/ontogpt/environmental-sample/> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ], - [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -sample:Study a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class sample:Measurement ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path sample:measurements ], - [ sh:class sample:CausalRelationship ; - sh:nodeKind sh:BlankNode ; - sh:order 3 ; - sh:path sample:causal_relationships ], - [ sh:class sample:Location ; - sh:description "the sites at which the study was conducted" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path sample:location ], - [ sh:class sample:Environment ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path sample:environments ], - [ sh:class sample:Variable ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path sample:variables ], - [ sh:class sample:EnvironmentalMaterial ; - sh:description "the environmental material that was sampled" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path sample:environmental_material ] ; - sh:targetClass sample:Study . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -sample:CausalRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class sample:Variable ; - sh:description "the variable that is the cause of the effect" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path sample:cause ], - [ sh:class sample:Variable ; - sh:description "the things that is affected" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path sample:effect ] ; - sh:targetClass sample:CausalRelationship . - -sample:Environment a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass sample:Environment . - -sample:EnvironmentalMaterial a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass sample:EnvironmentalMaterial . - -sample:Location a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass sample:Location . - -sample:Measurement a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "the value of the measurement" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path sample:value ], - [ sh:class sample:Unit ; - sh:description "the unit of the measurement" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path sample:unit ] ; - sh:targetClass sample:Measurement . - -sample:Unit a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass sample:Unit . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -sample:Variable a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass sample:Variable . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/environmental_sample/shex/environmental_sample.shex b/projects/environmental_sample/shex/environmental_sample.shex deleted file mode 100644 index 49dafa259..000000000 --- a/projects/environmental_sample/shex/environmental_sample.shex +++ /dev/null @@ -1,208 +0,0 @@ -BASE <http://w3id.org/ontogpt/environmental-sample/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<CausalRelationship> CLOSED { - ( $<CausalRelationship_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <cause> @<Variable> ? ; - <effect> @<Variable> ? - ) ; - rdf:type [ <CausalRelationship> ] ? - ) -} - -core:CompoundExpression ( - @<CausalRelationship> OR @<Measurement> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -<Environment> CLOSED { - ( $<Environment_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Environment> ] - ) -} - -<EnvironmentalMaterial> CLOSED { - ( $<EnvironmentalMaterial_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <EnvironmentalMaterial> ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<Location> CLOSED { - ( $<Location_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Location> ] - ) -} - -<Measurement> CLOSED { - ( $<Measurement_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <value> @linkml:String ? ; - <unit> @<Unit> ? - ) ; - rdf:type [ <Measurement> ] ? - ) -} - -core:NamedEntity ( - @<Environment> OR @<EnvironmentalMaterial> OR @<Location> OR @core:RelationshipType OR @<Unit> OR @<Variable> -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -<Study> CLOSED { - ( $<Study_tes> ( <location> @<Location> * ; - <environmental_material> @<EnvironmentalMaterial> * ; - <environments> @<Environment> * ; - <causal_relationships> @<CausalRelationship> * ; - <variables> @<Variable> * ; - <measurements> @<Measurement> * - ) ; - rdf:type [ <Study> ] ? - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - -<Unit> CLOSED { - ( $<Unit_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Unit> ] - ) -} - -<Variable> CLOSED { - ( $<Variable_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Variable> ] - ) -} - - diff --git a/projects/environmental_sample/sqlschema/environmental_sample.sql b/projects/environmental_sample/sqlschema/environmental_sample.sql deleted file mode 100644 index b76f935e7..000000000 --- a/projects/environmental_sample/sqlschema/environmental_sample.sql +++ /dev/null @@ -1,95 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Environment" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "EnvironmentalMaterial" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Location" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Study" ( - location TEXT, - environmental_material TEXT, - environments TEXT, - causal_relationships TEXT, - variables TEXT, - measurements TEXT, - PRIMARY KEY (location, environmental_material, environments, causal_relationships, variables, measurements) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Unit" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Variable" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "CausalRelationship" ( - cause TEXT, - effect TEXT, - PRIMARY KEY (cause, effect), - FOREIGN KEY(cause) REFERENCES "Variable" (id), - FOREIGN KEY(effect) REFERENCES "Variable" (id) -); - -CREATE TABLE "Measurement" ( - value TEXT, - unit TEXT, - PRIMARY KEY (value, unit), - FOREIGN KEY(unit) REFERENCES "Unit" (id) -); diff --git a/projects/gene_description_term/docs/AnnotatorResult.md b/projects/gene_description_term/docs/AnnotatorResult.md deleted file mode 100644 index b25d0a529..000000000 --- a/projects/gene_description_term/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [bp:AnnotatorResult](http://w3id.org/ontogpt/biological-process-templateAnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/gene_description_term/docs/Any.md b/projects/gene_description_term/docs/Any.md deleted file mode 100644 index cb46c4be4..000000000 --- a/projects/gene_description_term/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [bp:Any](http://w3id.org/ontogpt/biological-process-templateAny) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/gene_description_term/docs/CompoundExpression.md b/projects/gene_description_term/docs/CompoundExpression.md deleted file mode 100644 index 6c1bba32f..000000000 --- a/projects/gene_description_term/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [bp:CompoundExpression](http://w3id.org/ontogpt/biological-process-templateCompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/gene_description_term/docs/ExtractionResult.md b/projects/gene_description_term/docs/ExtractionResult.md deleted file mode 100644 index 4d0ab7ab9..000000000 --- a/projects/gene_description_term/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [bp:ExtractionResult](http://w3id.org/ontogpt/biological-process-templateExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/gene_description_term/docs/Gene.md b/projects/gene_description_term/docs/Gene.md deleted file mode 100644 index cd7be180a..000000000 --- a/projects/gene_description_term/docs/Gene.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Gene - - - - -URI: [bp:Gene](http://w3id.org/ontogpt/biological-process-templateGene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneDescription]-%20about%200..1>[Gene|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Gene],[GeneDescription])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneDescription]-%20about%200..1>[Gene|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Gene],[GeneDescription]) - -## Identifier prefixes - - * HGNC - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞about](geneDescription__about.md)* <sub>0..1</sub> **[Gene](Gene.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gene_description_term/docs/GeneDescription.md b/projects/gene_description_term/docs/GeneDescription.md deleted file mode 100644 index 2744f59a5..000000000 --- a/projects/gene_description_term/docs/GeneDescription.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: GeneDescription - - -A summarization of an individual gene - -URI: [bp:GeneDescription](http://w3id.org/ontogpt/biological-process-templateGeneDescription) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneDescriptionTerm],[GeneDescriptionTerm]<terms%200..*-%20[GeneDescription|narrative_summary:string%20%3F],[Gene]<about%200..1-%20[GeneDescription],[Gene])](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneDescriptionTerm],[GeneDescriptionTerm]<terms%200..*-%20[GeneDescription|narrative_summary:string%20%3F],[Gene]<about%200..1-%20[GeneDescription],[Gene]) - -## Attributes - - -### Own - - * [➞about](geneDescription__about.md) <sub>0..1</sub> - * Description: The official symbol of the gene that is described. For example "TP53". Do not include the word "gene" in the answer. - * Range: [Gene](Gene.md) - * [➞narrative_summary](geneDescription__narrative_summary.md) <sub>0..1</sub> - * Description: A free text summary describing the function of the gene - * Range: [String](types/String.md) - * [➞terms](geneDescription__terms.md) <sub>0..\*</sub> - * Description: A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene - * Range: [GeneDescriptionTerm](GeneDescriptionTerm.md) diff --git a/projects/gene_description_term/docs/GeneDescriptionTerm.md b/projects/gene_description_term/docs/GeneDescriptionTerm.md deleted file mode 100644 index 028c649b7..000000000 --- a/projects/gene_description_term/docs/GeneDescriptionTerm.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: GeneDescriptionTerm - - - - -URI: [bp:GeneDescriptionTerm](http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneDescription]-%20terms%200..*>[GeneDescriptionTerm|label:string%20%3F;id(i):string],[NamedEntity]^-[GeneDescriptionTerm],[GeneDescription])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneDescription]-%20terms%200..*>[GeneDescriptionTerm|label:string%20%3F;id(i):string],[NamedEntity]^-[GeneDescriptionTerm],[GeneDescription]) - -## Identifier prefixes - - * GO - * MONDO - * UBERON - * MESH - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞terms](geneDescription__terms.md)* <sub>0..\*</sub> **[GeneDescriptionTerm](GeneDescriptionTerm.md)** - -## Attributes - - -### Own - - * [➞label](geneDescriptionTerm__label.md) <sub>0..1</sub> - * Description: the name of the GO term - * Range: [String](types/String.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) diff --git a/projects/gene_description_term/docs/NamedEntity.md b/projects/gene_description_term/docs/NamedEntity.md deleted file mode 100644 index f65bbcc78..000000000 --- a/projects/gene_description_term/docs/NamedEntity.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [bp:NamedEntity](http://w3id.org/ontogpt/biological-process-templateNamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[GeneDescriptionTerm],[NamedEntity]^-[Gene],[Triple],[GeneDescriptionTerm],[Gene])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[GeneDescriptionTerm],[NamedEntity]^-[Gene],[Triple],[GeneDescriptionTerm],[Gene]) - -## Children - - * [Gene](Gene.md) - * [GeneDescriptionTerm](GeneDescriptionTerm.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gene_description_term/docs/NullDataOptions.md b/projects/gene_description_term/docs/NullDataOptions.md deleted file mode 100644 index 716244681..000000000 --- a/projects/gene_description_term/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [bp:NullDataOptions](http://w3id.org/ontogpt/biological-process-templateNullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/gene_description_term/docs/Publication.md b/projects/gene_description_term/docs/Publication.md deleted file mode 100644 index d54b928f4..000000000 --- a/projects/gene_description_term/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [bp:Publication](http://w3id.org/ontogpt/biological-process-templatePublication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/gene_description_term/docs/RelationshipType.md b/projects/gene_description_term/docs/RelationshipType.md deleted file mode 100644 index 918e3647c..000000000 --- a/projects/gene_description_term/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [bp:RelationshipType](http://w3id.org/ontogpt/biological-process-templateRelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gene_description_term/docs/TextWithTriples.md b/projects/gene_description_term/docs/TextWithTriples.md deleted file mode 100644 index 4237a7785..000000000 --- a/projects/gene_description_term/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [bp:TextWithTriples](http://w3id.org/ontogpt/biological-process-templateTextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/gene_description_term/docs/Triple.md b/projects/gene_description_term/docs/Triple.md deleted file mode 100644 index b9e6bb42d..000000000 --- a/projects/gene_description_term/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [bp:Triple](http://w3id.org/ontogpt/biological-process-templateTriple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/gene_description_term/docs/annotatorResult__object_id.md b/projects/gene_description_term/docs/annotatorResult__object_id.md deleted file mode 100644 index ffc6bbeca..000000000 --- a/projects/gene_description_term/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [bp:annotatorResult__object_id](http://w3id.org/ontogpt/biological-process-templateannotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/gene_description_term/docs/annotatorResult__object_text.md b/projects/gene_description_term/docs/annotatorResult__object_text.md deleted file mode 100644 index b127369af..000000000 --- a/projects/gene_description_term/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [bp:annotatorResult__object_text](http://w3id.org/ontogpt/biological-process-templateannotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/gene_description_term/docs/annotatorResult__subject_text.md b/projects/gene_description_term/docs/annotatorResult__subject_text.md deleted file mode 100644 index 79e732b09..000000000 --- a/projects/gene_description_term/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [bp:annotatorResult__subject_text](http://w3id.org/ontogpt/biological-process-templateannotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/gene_description_term/docs/extractionResult__extracted_object.md b/projects/gene_description_term/docs/extractionResult__extracted_object.md deleted file mode 100644 index 9cb7fab08..000000000 --- a/projects/gene_description_term/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [bp:extractionResult__extracted_object](http://w3id.org/ontogpt/biological-process-templateextractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gene_description_term/docs/extractionResult__input_id.md b/projects/gene_description_term/docs/extractionResult__input_id.md deleted file mode 100644 index 77a58c462..000000000 --- a/projects/gene_description_term/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [bp:extractionResult__input_id](http://w3id.org/ontogpt/biological-process-templateextractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gene_description_term/docs/extractionResult__input_text.md b/projects/gene_description_term/docs/extractionResult__input_text.md deleted file mode 100644 index 0d447a742..000000000 --- a/projects/gene_description_term/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [bp:extractionResult__input_text](http://w3id.org/ontogpt/biological-process-templateextractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gene_description_term/docs/extractionResult__input_title.md b/projects/gene_description_term/docs/extractionResult__input_title.md deleted file mode 100644 index 87d22e4d5..000000000 --- a/projects/gene_description_term/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [bp:extractionResult__input_title](http://w3id.org/ontogpt/biological-process-templateextractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gene_description_term/docs/extractionResult__named_entities.md b/projects/gene_description_term/docs/extractionResult__named_entities.md deleted file mode 100644 index 4274e9c2a..000000000 --- a/projects/gene_description_term/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [bp:extractionResult__named_entities](http://w3id.org/ontogpt/biological-process-templateextractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gene_description_term/docs/extractionResult__prompt.md b/projects/gene_description_term/docs/extractionResult__prompt.md deleted file mode 100644 index 2d9f03d71..000000000 --- a/projects/gene_description_term/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [bp:extractionResult__prompt](http://w3id.org/ontogpt/biological-process-templateextractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gene_description_term/docs/extractionResult__raw_completion_output.md b/projects/gene_description_term/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 0e689fc73..000000000 --- a/projects/gene_description_term/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [bp:extractionResult__raw_completion_output](http://w3id.org/ontogpt/biological-process-templateextractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gene_description_term/docs/geneDescriptionTerm__label.md b/projects/gene_description_term/docs/geneDescriptionTerm__label.md deleted file mode 100644 index 2f6e328d6..000000000 --- a/projects/gene_description_term/docs/geneDescriptionTerm__label.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: label - - -the name of the GO term - -URI: [bp:geneDescriptionTerm__label](http://w3id.org/ontogpt/biological-process-templategeneDescriptionTerm__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [GeneDescriptionTerm](GeneDescriptionTerm.md) diff --git a/projects/gene_description_term/docs/geneDescription__about.md b/projects/gene_description_term/docs/geneDescription__about.md deleted file mode 100644 index 5630fc47d..000000000 --- a/projects/gene_description_term/docs/geneDescription__about.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: about - - -The official symbol of the gene that is described. For example "TP53". Do not include the word "gene" in the answer. - -URI: [bp:geneDescription__about](http://w3id.org/ontogpt/biological-process-templategeneDescription__about) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneDescription](GeneDescription.md) diff --git a/projects/gene_description_term/docs/geneDescription__narrative_summary.md b/projects/gene_description_term/docs/geneDescription__narrative_summary.md deleted file mode 100644 index 7f5677e2e..000000000 --- a/projects/gene_description_term/docs/geneDescription__narrative_summary.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: narrative_summary - - -A free text summary describing the function of the gene - -URI: [bp:geneDescription__narrative_summary](http://w3id.org/ontogpt/biological-process-templategeneDescription__narrative_summary) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [GeneDescription](GeneDescription.md) diff --git a/projects/gene_description_term/docs/geneDescription__terms.md b/projects/gene_description_term/docs/geneDescription__terms.md deleted file mode 100644 index 9a45946fb..000000000 --- a/projects/gene_description_term/docs/geneDescription__terms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: terms - - -A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene - -URI: [bp:geneDescription__terms](http://w3id.org/ontogpt/biological-process-templategeneDescription__terms) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneDescriptionTerm](GeneDescriptionTerm.md) - -## Parents - - -## Children - - -## Used by - - * [GeneDescription](GeneDescription.md) diff --git a/projects/gene_description_term/docs/gene_description_term.md b/projects/gene_description_term/docs/gene_description_term.md deleted file mode 100644 index 410c3467d..000000000 --- a/projects/gene_description_term/docs/gene_description_term.md +++ /dev/null @@ -1,110 +0,0 @@ - -# go-term-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A simple GO term template for NER - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [GeneDescription](GeneDescription.md) - A summarization of an individual gene - * [NamedEntity](NamedEntity.md) - * [Gene](Gene.md) - * [GeneDescriptionTerm](GeneDescriptionTerm.md) - * [RelationshipType](RelationshipType.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞label](geneDescriptionTerm__label.md) - the name of the GO term - * [➞about](geneDescription__about.md) - The official symbol of the gene that is described. For example "TP53". Do not include the word "gene" in the answer. - * [➞narrative_summary](geneDescription__narrative_summary.md) - A free text summary describing the function of the gene - * [➞terms](geneDescription__terms.md) - A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/gene_description_term/docs/namedEntity__id.md b/projects/gene_description_term/docs/namedEntity__id.md deleted file mode 100644 index 4cf1e966f..000000000 --- a/projects/gene_description_term/docs/namedEntity__id.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [bp:namedEntity__id](http://w3id.org/ontogpt/biological-process-templatenamedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Gene](Gene.md) - * [GeneDescriptionTerm](GeneDescriptionTerm.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/gene_description_term/docs/namedEntity__label.md b/projects/gene_description_term/docs/namedEntity__label.md deleted file mode 100644 index ace66ab52..000000000 --- a/projects/gene_description_term/docs/namedEntity__label.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [bp:namedEntity__label](http://w3id.org/ontogpt/biological-process-templatenamedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Gene](Gene.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/gene_description_term/docs/publication__abstract.md b/projects/gene_description_term/docs/publication__abstract.md deleted file mode 100644 index 96be47057..000000000 --- a/projects/gene_description_term/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [bp:publication__abstract](http://w3id.org/ontogpt/biological-process-templatepublication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gene_description_term/docs/publication__combined_text.md b/projects/gene_description_term/docs/publication__combined_text.md deleted file mode 100644 index 613506acc..000000000 --- a/projects/gene_description_term/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [bp:publication__combined_text](http://w3id.org/ontogpt/biological-process-templatepublication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gene_description_term/docs/publication__full_text.md b/projects/gene_description_term/docs/publication__full_text.md deleted file mode 100644 index 978e83538..000000000 --- a/projects/gene_description_term/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [bp:publication__full_text](http://w3id.org/ontogpt/biological-process-templatepublication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gene_description_term/docs/publication__id.md b/projects/gene_description_term/docs/publication__id.md deleted file mode 100644 index 9c03571b0..000000000 --- a/projects/gene_description_term/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [bp:publication__id](http://w3id.org/ontogpt/biological-process-templatepublication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gene_description_term/docs/publication__title.md b/projects/gene_description_term/docs/publication__title.md deleted file mode 100644 index 93aa90543..000000000 --- a/projects/gene_description_term/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [bp:publication__title](http://w3id.org/ontogpt/biological-process-templatepublication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gene_description_term/docs/textWithTriples__publication.md b/projects/gene_description_term/docs/textWithTriples__publication.md deleted file mode 100644 index d5eb7b7f9..000000000 --- a/projects/gene_description_term/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [bp:textWithTriples__publication](http://w3id.org/ontogpt/biological-process-templatetextWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/gene_description_term/docs/textWithTriples__triples.md b/projects/gene_description_term/docs/textWithTriples__triples.md deleted file mode 100644 index 4865a084d..000000000 --- a/projects/gene_description_term/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [bp:textWithTriples__triples](http://w3id.org/ontogpt/biological-process-templatetextWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/gene_description_term/docs/triple__object.md b/projects/gene_description_term/docs/triple__object.md deleted file mode 100644 index bc102f3c8..000000000 --- a/projects/gene_description_term/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [bp:triple__object](http://w3id.org/ontogpt/biological-process-templatetriple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gene_description_term/docs/triple__object_qualifier.md b/projects/gene_description_term/docs/triple__object_qualifier.md deleted file mode 100644 index f06d74b8d..000000000 --- a/projects/gene_description_term/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [bp:triple__object_qualifier](http://w3id.org/ontogpt/biological-process-templatetriple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gene_description_term/docs/triple__predicate.md b/projects/gene_description_term/docs/triple__predicate.md deleted file mode 100644 index 92c257664..000000000 --- a/projects/gene_description_term/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [bp:triple__predicate](http://w3id.org/ontogpt/biological-process-templatetriple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gene_description_term/docs/triple__qualifier.md b/projects/gene_description_term/docs/triple__qualifier.md deleted file mode 100644 index 1ea0152f1..000000000 --- a/projects/gene_description_term/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [bp:triple__qualifier](http://w3id.org/ontogpt/biological-process-templatetriple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gene_description_term/docs/triple__subject.md b/projects/gene_description_term/docs/triple__subject.md deleted file mode 100644 index cc0377542..000000000 --- a/projects/gene_description_term/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [bp:triple__subject](http://w3id.org/ontogpt/biological-process-templatetriple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gene_description_term/docs/triple__subject_qualifier.md b/projects/gene_description_term/docs/triple__subject_qualifier.md deleted file mode 100644 index 998e0615e..000000000 --- a/projects/gene_description_term/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [bp:triple__subject_qualifier](http://w3id.org/ontogpt/biological-process-templatetriple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gene_description_term/docs/types/Boolean.md b/projects/gene_description_term/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/gene_description_term/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/gene_description_term/docs/types/Curie.md b/projects/gene_description_term/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/gene_description_term/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/gene_description_term/docs/types/Date.md b/projects/gene_description_term/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/gene_description_term/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/gene_description_term/docs/types/DateOrDatetime.md b/projects/gene_description_term/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/gene_description_term/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/gene_description_term/docs/types/Datetime.md b/projects/gene_description_term/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/gene_description_term/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/gene_description_term/docs/types/Decimal.md b/projects/gene_description_term/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/gene_description_term/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/gene_description_term/docs/types/Double.md b/projects/gene_description_term/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/gene_description_term/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/gene_description_term/docs/types/Float.md b/projects/gene_description_term/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/gene_description_term/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/gene_description_term/docs/types/Integer.md b/projects/gene_description_term/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/gene_description_term/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/gene_description_term/docs/types/Jsonpath.md b/projects/gene_description_term/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/gene_description_term/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/gene_description_term/docs/types/Jsonpointer.md b/projects/gene_description_term/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/gene_description_term/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/gene_description_term/docs/types/Ncname.md b/projects/gene_description_term/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/gene_description_term/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/gene_description_term/docs/types/Nodeidentifier.md b/projects/gene_description_term/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/gene_description_term/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/gene_description_term/docs/types/Objectidentifier.md b/projects/gene_description_term/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/gene_description_term/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/gene_description_term/docs/types/Sparqlpath.md b/projects/gene_description_term/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/gene_description_term/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/gene_description_term/docs/types/String.md b/projects/gene_description_term/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/gene_description_term/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/gene_description_term/docs/types/Time.md b/projects/gene_description_term/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/gene_description_term/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/gene_description_term/docs/types/Uri.md b/projects/gene_description_term/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/gene_description_term/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/gene_description_term/docs/types/Uriorcurie.md b/projects/gene_description_term/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/gene_description_term/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/gene_description_term/excel/gene_description_term.xlsx b/projects/gene_description_term/excel/gene_description_term.xlsx deleted file mode 100644 index c249ee2a279d55b7d337d21be5d58630ee9bd0cb..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 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date: 2023-08-07T10:53:31 -# Schema: go-term-template -# -# id: https://w3id.org/ontogpt/go_term -# description: A simple GO term template for NER -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -GO = CurieNamespace('GO', 'http://purl.obolibrary.org/obo/GO_') -HGNC = CurieNamespace('HGNC', 'http://identifiers.org/hgnc/') -MESH = CurieNamespace('MESH', 'http://identifiers.org/mesh/') -MONDO = CurieNamespace('MONDO', 'http://purl.obolibrary.org/obo/MONDO_') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -UBERON = CurieNamespace('UBERON', 'http://example.org/UNKNOWN/UBERON/') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -BP = CurieNamespace('bp', 'http://w3id.org/ontogpt/biological-process-template') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = BP - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class GeneId(NamedEntityId): - pass - - -class GeneDescriptionTermId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class GeneDescription(YAMLRoot): - """ - A summarization of an individual gene - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.GeneDescription - class_class_curie: ClassVar[str] = "bp:GeneDescription" - class_name: ClassVar[str] = "GeneDescription" - class_model_uri: ClassVar[URIRef] = BP.GeneDescription - - about: Optional[Union[str, GeneId]] = None - narrative_summary: Optional[str] = None - terms: Optional[Union[Union[str, GeneDescriptionTermId], List[Union[str, GeneDescriptionTermId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.about is not None and not isinstance(self.about, GeneId): - self.about = GeneId(self.about) - - if self.narrative_summary is not None and not isinstance(self.narrative_summary, str): - self.narrative_summary = str(self.narrative_summary) - - if not isinstance(self.terms, list): - self.terms = [self.terms] if self.terms is not None else [] - self.terms = [v if isinstance(v, GeneDescriptionTermId) else GeneDescriptionTermId(v) for v in self.terms] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = BP.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = BP.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.Gene - class_class_curie: ClassVar[str] = "bp:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = BP.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneDescriptionTerm(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.GeneDescriptionTerm - class_class_curie: ClassVar[str] = "bp:GeneDescriptionTerm" - class_name: ClassVar[str] = "GeneDescriptionTerm" - class_model_uri: ClassVar[URIRef] = BP.GeneDescriptionTerm - - id: Union[str, GeneDescriptionTermId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneDescriptionTermId): - self.id = GeneDescriptionTermId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = BP.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = BP.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = BP.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = BP.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = BP.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = BP.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.geneDescription__about = Slot(uri=BP.about, name="geneDescription__about", curie=BP.curie('about'), - model_uri=BP.geneDescription__about, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneDescription__narrative_summary = Slot(uri=BP.narrative_summary, name="geneDescription__narrative_summary", curie=BP.curie('narrative_summary'), - model_uri=BP.geneDescription__narrative_summary, domain=None, range=Optional[str]) - -slots.geneDescription__terms = Slot(uri=BP.terms, name="geneDescription__terms", curie=BP.curie('terms'), - model_uri=BP.geneDescription__terms, domain=None, range=Optional[Union[Union[str, GeneDescriptionTermId], List[Union[str, GeneDescriptionTermId]]]]) - -slots.geneDescriptionTerm__label = Slot(uri=BP.label, name="geneDescriptionTerm__label", curie=BP.curie('label'), - model_uri=BP.geneDescriptionTerm__label, domain=None, range=Optional[str]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=BP.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=BP.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=BP.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=BP.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=BP.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=BP.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=BP.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=BP.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=BP.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=BP.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=BP.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=BP.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=BP.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=BP.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=BP.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=BP.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=BP.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=BP.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=BP.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=BP.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=BP.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=BP.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=BP.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=BP.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=BP.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/gene_description_term/graphql/gene_description_term.graphql b/projects/gene_description_term/graphql/gene_description_term.graphql deleted file mode 100644 index 70be47e72..000000000 --- a/projects/gene_description_term/graphql/gene_description_term.graphql +++ /dev/null @@ -1,82 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Gene - { - id: String! - label: String - } - -type GeneDescription - { - about: Gene - narrativeSummary: String - terms: [GeneDescriptionTerm] - } - -type GeneDescriptionTerm - { - id: String! - label: String - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/gene_description_term/jsonld/gene_description_term.context.jsonld b/projects/gene_description_term/jsonld/gene_description_term.context.jsonld deleted file mode 100644 index c01be5aa2..000000000 --- a/projects/gene_description_term/jsonld/gene_description_term.context.jsonld +++ /dev/null @@ -1,147 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:53:23", - "source": "gene_description_term.yaml" - }, - "@context": { - "GO": { - "@id": "http://purl.obolibrary.org/obo/GO_", - "@prefix": true - }, - "HGNC": "http://identifiers.org/hgnc/", - "MESH": "http://identifiers.org/mesh/", - "MONDO": { - "@id": "http://purl.obolibrary.org/obo/MONDO_", - "@prefix": true - }, - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "UBERON": "http://example.org/UNKNOWN/UBERON/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "bp": { - "@id": "http://w3id.org/ontogpt/biological-process-template", - "@prefix": true - }, - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/biological-process-template", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "about": { - "@type": "@id" - }, - "terms": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/gene_description_term/jsonld/gene_description_term.jsonld b/projects/gene_description_term/jsonld/gene_description_term.jsonld deleted file mode 100644 index 96affc5f4..000000000 --- a/projects/gene_description_term/jsonld/gene_description_term.jsonld +++ /dev/null @@ -1,1132 +0,0 @@ -{ - "name": "go-term-template", - "description": "A simple GO term template for NER", - "title": "GO Term Template", - "id": "https://w3id.org/ontogpt/go_term", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "bp", - "prefix_reference": "http://w3id.org/ontogpt/biological-process-template" - }, - { - "prefix_prefix": "HGNC", - "prefix_reference": "http://identifiers.org/hgnc/" - }, - { - "prefix_prefix": "GO", - "prefix_reference": "http://purl.obolibrary.org/obo/GO_" - }, - { - "prefix_prefix": "MONDO", - "prefix_reference": "http://purl.obolibrary.org/obo/MONDO_" - }, - { - "prefix_prefix": "MESH", - "prefix_reference": "http://identifiers.org/mesh/" - } - ], - "default_prefix": "bp", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "geneDescription__about", - "description": "The official symbol of the gene that is described. For example \"TP53\". Do not include the word \"gene\" in the answer.", - "from_schema": "https://w3id.org/ontogpt/go_term", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templateabout", - "alias": "about", - "owner": "GeneDescription", - "domain_of": [ - "GeneDescription" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneDescription__narrative_summary", - "description": "A free text summary describing the function of the gene", - "from_schema": "https://w3id.org/ontogpt/go_term", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templatenarrative_summary", - "alias": "narrative_summary", - "owner": "GeneDescription", - "domain_of": [ - "GeneDescription" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "geneDescription__terms", - "description": "A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene", - "from_schema": "https://w3id.org/ontogpt/go_term", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templateterms", - "multivalued": true, - "alias": "terms", - "owner": "GeneDescription", - "domain_of": [ - "GeneDescription" - ], - "range": "GeneDescriptionTerm", - "@type": "SlotDefinition" - }, - { - "name": "geneDescriptionTerm__label", - "description": "the name of the GO term", - "from_schema": "https://w3id.org/ontogpt/go_term", - "slot_uri": "http://w3id.org/ontogpt/biological-process-templatelabel", - "alias": "label", - "owner": "GeneDescriptionTerm", - "domain_of": [ - "GeneDescriptionTerm" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Gene", - "id_prefixes": [ - "HGNC" - ], - "definition_uri": "http://w3id.org/ontogpt/biological-process-templateGene", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:hgnc", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/go_term", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/biological-process-templateGene", - "@type": "ClassDefinition" - }, - { - "name": "GeneDescription", - "definition_uri": "http://w3id.org/ontogpt/biological-process-templateGeneDescription", - "description": "A summarization of an individual gene", - "from_schema": "https://w3id.org/ontogpt/go_term", - "slots": [ - "geneDescription__about", - "geneDescription__narrative_summary", - "geneDescription__terms" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "about", - "description": "The official symbol of the gene that is described. For example \"TP53\". Do not include the word \"gene\" in the answer.", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "narrative_summary", - "description": "A free text summary describing the function of the gene", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "terms", - "description": "A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene", - "multivalued": true, - "range": "GeneDescriptionTerm", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/biological-process-templateGeneDescription", - "@type": "ClassDefinition" - }, - { - "name": "GeneDescriptionTerm", - "id_prefixes": [ - "GO", - "MONDO", - "UBERON", - "MESH" - ], - "definition_uri": "http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go, sqlite:obo:mondo, sqlite:obo:uberon, sqlite:obo:mesh", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/go_term", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "geneDescriptionTerm__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "label", - "description": "the name of the GO term", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "gene_description_term.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 1614, - "generation_date": "2023-08-07T10:53:24", - "@type": "SchemaDefinition", - "@context": [ - "projects/gene_description_term/jsonld/gene_description_term.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/biological-process-template" - } - ] -} diff --git a/projects/gene_description_term/jsonschema/gene_description_term.schema.json b/projects/gene_description_term/jsonschema/gene_description_term.schema.json deleted file mode 100644 index c098ee47a..000000000 --- a/projects/gene_description_term/jsonschema/gene_description_term.schema.json +++ /dev/null @@ -1,215 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Gene": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Gene", - "type": "object" - }, - "GeneDescription": { - "additionalProperties": false, - "description": "A summarization of an individual gene", - "properties": { - "about": { - "description": "The official symbol of the gene that is described. For example \"TP53\". Do not include the word \"gene\" in the answer.", - "type": "string" - }, - "narrative_summary": { - "description": "A free text summary describing the function of the gene", - "type": "string" - }, - "terms": { - "description": "A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "GeneDescription", - "type": "object" - }, - "GeneDescriptionTerm": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "the name of the GO term", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "GeneDescriptionTerm", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "https://w3id.org/ontogpt/go_term", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "the name of the GO term", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "go-term-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/gene_description_term/owl/gene_description_term.owl.ttl b/projects/gene_description_term/owl/gene_description_term.owl.ttl deleted file mode 100644 index fb63ae60d..000000000 --- a/projects/gene_description_term/owl/gene_description_term.owl.ttl +++ /dev/null @@ -1,415 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix bp: <http://w3id.org/ontogpt/biological-process-template> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<https://w3id.org/ontogpt/go_term> a owl:Ontology ; - rdfs:label "go-term-template" ; - IAO:0000700 bp:GeneDescription, - <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples> ; - linkml:classes "{'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC'], definition_uri='http://w3id.org/ontogpt/biological-process-templateGene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hgnc', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/go_term', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='bp:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneDescription': ClassDefinition(name='GeneDescription', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/biological-process-templateGeneDescription', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A summarization of an individual gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/go_term', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneDescription__about', 'geneDescription__narrative_summary', 'geneDescription__terms'], slot_usage={}, attributes={'about': SlotDefinition(name='about', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The official symbol of the gene that is described. For example \"TP53\". Do not include the word \"gene\" in the answer.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'narrative_summary': SlotDefinition(name='narrative_summary', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A free text summary describing the function of the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'terms': SlotDefinition(name='terms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneDescriptionTerm', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='bp:GeneDescription', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneDescriptionTerm': ClassDefinition(name='GeneDescriptionTerm', id_prefixes=['GO', 'MONDO', 'UBERON', 'MESH'], definition_uri='http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:mondo, sqlite:obo:uberon, sqlite:obo:mesh', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/go_term', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'geneDescriptionTerm__label'], slot_usage={}, attributes={'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the GO term', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='bp:GeneDescriptionTerm', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/go_term" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -bp:GeneDescription a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneDescription" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty bp:narrative_summary ], - [ a owl:Restriction ; - owl:allValuesFrom bp:GeneDescriptionTerm ; - owl:onProperty bp:terms ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass bp:Gene ; - owl:onProperty bp:about ] ; - skos:definition "A summarization of an individual gene" ; - linkml:attributes "{'about': SlotDefinition(name='about', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The official symbol of the gene that is described. For example \"TP53\". Do not include the word \"gene\" in the answer.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'narrative_summary': SlotDefinition(name='narrative_summary', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A free text summary describing the function of the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'terms': SlotDefinition(name='terms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneDescriptionTerm', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -bp:about a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "about" ; - rdfs:range bp:Gene ; - skos:definition "The official symbol of the gene that is described. For example \"TP53\". Do not include the word \"gene\" in the answer." . - -bp:label a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - rdfs:range linkml:String ; - skos:definition "the name of the GO term" . - -bp:narrative_summary a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "narrative_summary" ; - rdfs:range linkml:String ; - skos:definition "A free text summary describing the function of the gene" . - -bp:terms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "terms" ; - rdfs:range bp:GeneDescriptionTerm ; - skos:definition "A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - bp:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - bp:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -bp:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - bp:annotators "sqlite:obo:hgnc" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -bp:GeneDescriptionTerm a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneDescriptionTerm" ; - bp:annotators "sqlite:obo:go, sqlite:obo:mondo, sqlite:obo:uberon, sqlite:obo:mesh" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty bp:label ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the GO term', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/gene_description_term/prefixmap/gene_description_term.yaml b/projects/gene_description_term/prefixmap/gene_description_term.yaml deleted file mode 100644 index 0ea758005..000000000 --- a/projects/gene_description_term/prefixmap/gene_description_term.yaml +++ /dev/null @@ -1,40 +0,0 @@ -{ - "GO": "http://purl.obolibrary.org/obo/GO_", - "HGNC": "http://identifiers.org/hgnc/", - "MESH": "http://identifiers.org/mesh/", - "MONDO": "http://purl.obolibrary.org/obo/MONDO_", - "RO": "http://purl.obolibrary.org/obo/RO_", - "UBERON": "http://example.org/UNKNOWN/UBERON/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "bp": "http://w3id.org/ontogpt/biological-process-template", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/gene_description_term/protobuf/gene_description_term.proto b/projects/gene_description_term/protobuf/gene_description_term.proto deleted file mode 100644 index 7d2bd9128..000000000 --- a/projects/gene_description_term/protobuf/gene_description_term.proto +++ /dev/null @@ -1,52 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -// A summarization of an individual gene -message GeneDescription - { - gene about = 0 - string narrativeSummary = 0 - repeated geneDescriptionTerm terms = 0 - } -message GeneDescriptionTerm - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/gene_description_term/shacl/gene_description_term.shacl.ttl b/projects/gene_description_term/shacl/gene_description_term.shacl.ttl deleted file mode 100644 index e33c3129c..000000000 --- a/projects/gene_description_term/shacl/gene_description_term.shacl.ttl +++ /dev/null @@ -1,213 +0,0 @@ -@prefix bp: <http://w3id.org/ontogpt/biological-process-template> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -bp:GeneDescription a sh:NodeShape ; - sh:closed true ; - sh:description "A summarization of an individual gene" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class bp:Gene ; - sh:description "The official symbol of the gene that is described. For example \"TP53\". Do not include the word \"gene\" in the answer." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path bp:about ], - [ sh:class bp:GeneDescriptionTerm ; - sh:description "A semicolon separated list of controlled terms drawn from the Gene Ontology that describe the function of the gene" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path bp:terms ], - [ sh:description "A free text summary describing the function of the gene" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path bp:narrative_summary ] ; - sh:targetClass bp:GeneDescription . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -bp:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass bp:Gene . - -bp:GeneDescriptionTerm a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "the name of the GO term" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path bp:label ] ; - sh:targetClass bp:GeneDescriptionTerm . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/gene_description_term/shex/gene_description_term.shex b/projects/gene_description_term/shex/gene_description_term.shex deleted file mode 100644 index 83279f026..000000000 --- a/projects/gene_description_term/shex/gene_description_term.shex +++ /dev/null @@ -1,163 +0,0 @@ -BASE <http://w3id.org/ontogpt/biological-process-template/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<http://w3id.org/ontogpt/biological-process-templateGene> CLOSED { - ( $<http://w3id.org/ontogpt/biological-process-templateGene_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/biological-process-templateGene> ] - ) -} - -<http://w3id.org/ontogpt/biological-process-templateGeneDescription> CLOSED { - ( $<http://w3id.org/ontogpt/biological-process-templateGeneDescription_tes> ( - <http://w3id.org/ontogpt/biological-process-templateabout> @<http://w3id.org/ontogpt/biological-process-templateGene> ? ; - <http://w3id.org/ontogpt/biological-process-templatenarrative_summary> @linkml:String ? ; - <http://w3id.org/ontogpt/biological-process-templateterms> - @<http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm> * - ) ; - rdf:type [ <http://w3id.org/ontogpt/biological-process-templateGeneDescription> ] ? - ) -} - -<http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm> CLOSED { - ( $<http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - <http://w3id.org/ontogpt/biological-process-templatelabel> @linkml:String ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm> ] - ) -} - -core:NamedEntity ( - @<http://w3id.org/ontogpt/biological-process-templateGene> OR - @<http://w3id.org/ontogpt/biological-process-templateGeneDescriptionTerm> OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/gene_description_term/sqlschema/gene_description_term.sql b/projects/gene_description_term/sqlschema/gene_description_term.sql deleted file mode 100644 index 37e47244b..000000000 --- a/projects/gene_description_term/sqlschema/gene_description_term.sql +++ /dev/null @@ -1,60 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "GeneDescriptionTerm" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "GeneDescription" ( - about TEXT, - narrative_summary TEXT, - terms TEXT, - PRIMARY KEY (about, narrative_summary, terms), - FOREIGN KEY(about) REFERENCES "Gene" (id) -); diff --git a/projects/gocam/docs/AnnotatorResult.md b/projects/gocam/docs/AnnotatorResult.md deleted file mode 100644 index b21f75a37..000000000 --- a/projects/gocam/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [gocam:AnnotatorResult](http://w3id.org/ontogpt/gocam/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/Any.md b/projects/gocam/docs/Any.md deleted file mode 100644 index 294c64451..000000000 --- a/projects/gocam/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [gocam:Any](http://w3id.org/ontogpt/gocam/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/gocam/docs/CellType.md b/projects/gocam/docs/CellType.md deleted file mode 100644 index cce37c2b0..000000000 --- a/projects/gocam/docs/CellType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: CellType - - - - -URI: [gocam:CellType](http://w3id.org/ontogpt/gocam/CellType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/gocam/docs/CellularProcess.md b/projects/gocam/docs/CellularProcess.md deleted file mode 100644 index 6655db07f..000000000 --- a/projects/gocam/docs/CellularProcess.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: CellularProcess - - - - -URI: [gocam:CellularProcess](http://w3id.org/ontogpt/gocam/CellularProcess) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GoCamAnnotations]-%20cellular_processes%200..*>[CellularProcess|id(i):string;label(i):string%20%3F],[NamedEntity]^-[CellularProcess],[GoCamAnnotations])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GoCamAnnotations]-%20cellular_processes%200..*>[CellularProcess|id(i):string;label(i):string%20%3F],[NamedEntity]^-[CellularProcess],[GoCamAnnotations]) - -## Identifier prefixes - - * GO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞cellular_processes](goCamAnnotations__cellular_processes.md)* <sub>0..\*</sub> **[CellularProcess](CellularProcess.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/CompoundExpression.md b/projects/gocam/docs/CompoundExpression.md deleted file mode 100644 index 2c710a723..000000000 --- a/projects/gocam/docs/CompoundExpression.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [gocam:CompoundExpression](http://w3id.org/ontogpt/gocam/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship],[GeneGeneInteraction],[CompoundExpression]^-[Triple],[CompoundExpression]^-[GeneSubcellularLocalizationRelationship],[CompoundExpression]^-[GeneOrganismRelationship],[CompoundExpression]^-[GeneMolecularActivityRelationship2],[CompoundExpression]^-[GeneMolecularActivityRelationship],[CompoundExpression]^-[GeneGeneInteraction])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship],[GeneGeneInteraction],[CompoundExpression]^-[Triple],[CompoundExpression]^-[GeneSubcellularLocalizationRelationship],[CompoundExpression]^-[GeneOrganismRelationship],[CompoundExpression]^-[GeneMolecularActivityRelationship2],[CompoundExpression]^-[GeneMolecularActivityRelationship],[CompoundExpression]^-[GeneGeneInteraction]) - -## Children - - * [GeneGeneInteraction](GeneGeneInteraction.md) - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) - * [GeneOrganismRelationship](GeneOrganismRelationship.md) - * [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/gocam/docs/ExtractionResult.md b/projects/gocam/docs/ExtractionResult.md deleted file mode 100644 index 5fd1b0627..000000000 --- a/projects/gocam/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [gocam:ExtractionResult](http://w3id.org/ontogpt/gocam/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/gocam/docs/GOCellComponentType.md b/projects/gocam/docs/GOCellComponentType.md deleted file mode 100644 index e2e6fcda9..000000000 --- a/projects/gocam/docs/GOCellComponentType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: GOCellComponentType - - - - -URI: [gocam:GOCellComponentType](http://w3id.org/ontogpt/gocam/GOCellComponentType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/gocam/docs/Gene.md b/projects/gocam/docs/Gene.md deleted file mode 100644 index 2a66c7056..000000000 --- a/projects/gocam/docs/Gene.md +++ /dev/null @@ -1,42 +0,0 @@ - -# Class: Gene - - - - -URI: [gocam:Gene](http://w3id.org/ontogpt/gocam/Gene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneGeneInteraction]-%20gene1%200..1>[Gene|id(i):string;label(i):string%20%3F],[GeneGeneInteraction]-%20gene2%200..1>[Gene],[GeneMolecularActivityRelationship2]-%20gene%200..1>[Gene],[GeneMolecularActivityRelationship]-%20gene%200..1>[Gene],[GeneOrganismRelationship]-%20gene%200..1>[Gene],[GeneSubcellularLocalizationRelationship]-%20gene%200..1>[Gene],[GoCamAnnotations]-%20genes%200..*>[Gene],[NamedEntity]^-[Gene],[GoCamAnnotations],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship],[GeneGeneInteraction])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneGeneInteraction]-%20gene1%200..1>[Gene|id(i):string;label(i):string%20%3F],[GeneGeneInteraction]-%20gene2%200..1>[Gene],[GeneMolecularActivityRelationship2]-%20gene%200..1>[Gene],[GeneMolecularActivityRelationship]-%20gene%200..1>[Gene],[GeneOrganismRelationship]-%20gene%200..1>[Gene],[GeneSubcellularLocalizationRelationship]-%20gene%200..1>[Gene],[GoCamAnnotations]-%20genes%200..*>[Gene],[NamedEntity]^-[Gene],[GoCamAnnotations],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship],[GeneGeneInteraction]) - -## Identifier prefixes - - * HGNC - * PR - * UniProtKB - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞gene1](geneGeneInteraction__gene1.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene2](geneGeneInteraction__gene2.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneMolecularActivityRelationship2__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneMolecularActivityRelationship__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneOrganismRelationship__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneSubcellularLocalizationRelationship__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞genes](goCamAnnotations__genes.md)* <sub>0..\*</sub> **[Gene](Gene.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/GeneGeneInteraction.md b/projects/gocam/docs/GeneGeneInteraction.md deleted file mode 100644 index 579fc263d..000000000 --- a/projects/gocam/docs/GeneGeneInteraction.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: GeneGeneInteraction - - - - -URI: [gocam:GeneGeneInteraction](http://w3id.org/ontogpt/gocam/GeneGeneInteraction) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Gene]<gene2%200..1-%20[GeneGeneInteraction],[Gene]<gene1%200..1-%20[GeneGeneInteraction],[GoCamAnnotations]++-%20gene_gene_interactions%200..*>[GeneGeneInteraction],[CompoundExpression]^-[GeneGeneInteraction],[GoCamAnnotations],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Gene]<gene2%200..1-%20[GeneGeneInteraction],[Gene]<gene1%200..1-%20[GeneGeneInteraction],[GoCamAnnotations]++-%20gene_gene_interactions%200..*>[GeneGeneInteraction],[CompoundExpression]^-[GeneGeneInteraction],[GoCamAnnotations],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_gene_interactions](goCamAnnotations__gene_gene_interactions.md)* <sub>0..\*</sub> **[GeneGeneInteraction](GeneGeneInteraction.md)** - -## Attributes - - -### Own - - * [➞gene1](geneGeneInteraction__gene1.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞gene2](geneGeneInteraction__gene2.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) diff --git a/projects/gocam/docs/GeneLocation.md b/projects/gocam/docs/GeneLocation.md deleted file mode 100644 index d54b4da61..000000000 --- a/projects/gocam/docs/GeneLocation.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Class: GeneLocation - - - - -URI: [gocam:GeneLocation](http://w3id.org/ontogpt/gocam/GeneLocation) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneSubcellularLocalizationRelationship]-%20location%200..1>[GeneLocation|id:string;label(i):string%20%3F],[NamedEntity]^-[GeneLocation],[GeneSubcellularLocalizationRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneSubcellularLocalizationRelationship]-%20location%200..1>[GeneLocation|id:string;label(i):string%20%3F],[NamedEntity]^-[GeneLocation],[GeneSubcellularLocalizationRelationship]) - -## Identifier prefixes - - * GO - * CL - * UBERON - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞location](geneSubcellularLocalizationRelationship__location.md)* <sub>0..1</sub> **[GeneLocation](GeneLocation.md)** - -## Attributes - - -### Own - - * [GeneLocation➞id](GeneLocation_id.md) <sub>1..1</sub> - * Range: [String](types/String.md) - -### Inherited from NamedEntity: - - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/GeneLocationEnum.md b/projects/gocam/docs/GeneLocationEnum.md deleted file mode 100644 index 67626c0d9..000000000 --- a/projects/gocam/docs/GeneLocationEnum.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: GeneLocationEnum - - - - -URI: [gocam:GeneLocationEnum](http://w3id.org/ontogpt/gocam/GeneLocationEnum) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/gocam/docs/GeneLocation_id.md b/projects/gocam/docs/GeneLocation_id.md deleted file mode 100644 index 1357ee5d7..000000000 --- a/projects/gocam/docs/GeneLocation_id.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: id - - - - -URI: [gocam:GeneLocation_id](http://w3id.org/ontogpt/gocam/GeneLocation_id) - - -## Domain and Range - -[GeneLocation](GeneLocation.md) → <sub>1..1</sub> [String](types/String.md) - -## Parents - - * is_a: [➞id](namedEntity__id.md) - -## Children - - -## Used by - - * [GeneLocation](GeneLocation.md) diff --git a/projects/gocam/docs/GeneMolecularActivityRelationship.md b/projects/gocam/docs/GeneMolecularActivityRelationship.md deleted file mode 100644 index b605122de..000000000 --- a/projects/gocam/docs/GeneMolecularActivityRelationship.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: GeneMolecularActivityRelationship - - - - -URI: [gocam:GeneMolecularActivityRelationship](http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[MolecularActivity],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship],[GoCamAnnotations]++-%20gene_functions%200..*>[GeneMolecularActivityRelationship],[CompoundExpression]^-[GeneMolecularActivityRelationship],[GoCamAnnotations],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[MolecularActivity],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship],[GoCamAnnotations]++-%20gene_functions%200..*>[GeneMolecularActivityRelationship],[CompoundExpression]^-[GeneMolecularActivityRelationship],[GoCamAnnotations],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_functions](goCamAnnotations__gene_functions.md)* <sub>0..\*</sub> **[GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md)** - -## Attributes - - -### Own - - * [➞gene](geneMolecularActivityRelationship__gene.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md) <sub>0..1</sub> - * Range: [MolecularActivity](MolecularActivity.md) diff --git a/projects/gocam/docs/GeneMolecularActivityRelationship2.md b/projects/gocam/docs/GeneMolecularActivityRelationship2.md deleted file mode 100644 index 395313a4f..000000000 --- a/projects/gocam/docs/GeneMolecularActivityRelationship2.md +++ /dev/null @@ -1,26 +0,0 @@ - -# Class: GeneMolecularActivityRelationship2 - - - - -URI: [gocam:GeneMolecularActivityRelationship2](http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship2) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Molecule],[MolecularActivity],[Molecule]<target%200..1-%20[GeneMolecularActivityRelationship2],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship2],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship2],[CompoundExpression]^-[GeneMolecularActivityRelationship2],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Molecule],[MolecularActivity],[Molecule]<target%200..1-%20[GeneMolecularActivityRelationship2],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship2],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship2],[CompoundExpression]^-[GeneMolecularActivityRelationship2],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Attributes - - -### Own - - * [➞gene](geneMolecularActivityRelationship2__gene.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship2__molecular_activity.md) <sub>0..1</sub> - * Range: [MolecularActivity](MolecularActivity.md) - * [➞target](geneMolecularActivityRelationship2__target.md) <sub>0..1</sub> - * Range: [Molecule](Molecule.md) diff --git a/projects/gocam/docs/GeneOrganismRelationship.md b/projects/gocam/docs/GeneOrganismRelationship.md deleted file mode 100644 index 652185c57..000000000 --- a/projects/gocam/docs/GeneOrganismRelationship.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: GeneOrganismRelationship - - - - -URI: [gocam:GeneOrganismRelationship](http://w3id.org/ontogpt/gocam/GeneOrganismRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Organism],[Organism]<organism%200..1-%20[GeneOrganismRelationship],[Gene]<gene%200..1-%20[GeneOrganismRelationship],[GoCamAnnotations]++-%20gene_organisms%200..*>[GeneOrganismRelationship],[CompoundExpression]^-[GeneOrganismRelationship],[GoCamAnnotations],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Organism],[Organism]<organism%200..1-%20[GeneOrganismRelationship],[Gene]<gene%200..1-%20[GeneOrganismRelationship],[GoCamAnnotations]++-%20gene_organisms%200..*>[GeneOrganismRelationship],[CompoundExpression]^-[GeneOrganismRelationship],[GoCamAnnotations],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_organisms](goCamAnnotations__gene_organisms.md)* <sub>0..\*</sub> **[GeneOrganismRelationship](GeneOrganismRelationship.md)** - -## Attributes - - -### Own - - * [➞gene](geneOrganismRelationship__gene.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞organism](geneOrganismRelationship__organism.md) <sub>0..1</sub> - * Range: [Organism](Organism.md) diff --git a/projects/gocam/docs/GeneSubcellularLocalizationRelationship.md b/projects/gocam/docs/GeneSubcellularLocalizationRelationship.md deleted file mode 100644 index d9f8648b4..000000000 --- a/projects/gocam/docs/GeneSubcellularLocalizationRelationship.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: GeneSubcellularLocalizationRelationship - - - - -URI: [gocam:GeneSubcellularLocalizationRelationship](http://w3id.org/ontogpt/gocam/GeneSubcellularLocalizationRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneLocation]<location%200..1-%20[GeneSubcellularLocalizationRelationship],[Gene]<gene%200..1-%20[GeneSubcellularLocalizationRelationship],[GoCamAnnotations]++-%20gene_localizations%200..*>[GeneSubcellularLocalizationRelationship],[CompoundExpression]^-[GeneSubcellularLocalizationRelationship],[GoCamAnnotations],[GeneLocation],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneLocation]<location%200..1-%20[GeneSubcellularLocalizationRelationship],[Gene]<gene%200..1-%20[GeneSubcellularLocalizationRelationship],[GoCamAnnotations]++-%20gene_localizations%200..*>[GeneSubcellularLocalizationRelationship],[CompoundExpression]^-[GeneSubcellularLocalizationRelationship],[GoCamAnnotations],[GeneLocation],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_localizations](goCamAnnotations__gene_localizations.md)* <sub>0..\*</sub> **[GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md)** - -## Attributes - - -### Own - - * [➞gene](geneSubcellularLocalizationRelationship__gene.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞location](geneSubcellularLocalizationRelationship__location.md) <sub>0..1</sub> - * Range: [GeneLocation](GeneLocation.md) diff --git a/projects/gocam/docs/GoCamAnnotations.md b/projects/gocam/docs/GoCamAnnotations.md deleted file mode 100644 index e23722b20..000000000 --- a/projects/gocam/docs/GoCamAnnotations.md +++ /dev/null @@ -1,42 +0,0 @@ - -# Class: GoCamAnnotations - - - - -URI: [gocam:GoCamAnnotations](http://w3id.org/ontogpt/gocam/GoCamAnnotations) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Pathway],[Organism],[MolecularActivity],[GeneSubcellularLocalizationRelationship]<gene_localizations%200..*-++[GoCamAnnotations],[GeneGeneInteraction]<gene_gene_interactions%200..*-++[GoCamAnnotations],[Pathway]<pathways%200..*-%20[GoCamAnnotations],[CellularProcess]<cellular_processes%200..*-%20[GoCamAnnotations],[GeneMolecularActivityRelationship]<gene_functions%200..*-++[GoCamAnnotations],[MolecularActivity]<activities%200..*-%20[GoCamAnnotations],[GeneOrganismRelationship]<gene_organisms%200..*-++[GoCamAnnotations],[Organism]<organisms%200..*-%20[GoCamAnnotations],[Gene]<genes%200..*-%20[GoCamAnnotations],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship],[GeneGeneInteraction],[Gene],[CellularProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[Pathway],[Organism],[MolecularActivity],[GeneSubcellularLocalizationRelationship]<gene_localizations%200..*-++[GoCamAnnotations],[GeneGeneInteraction]<gene_gene_interactions%200..*-++[GoCamAnnotations],[Pathway]<pathways%200..*-%20[GoCamAnnotations],[CellularProcess]<cellular_processes%200..*-%20[GoCamAnnotations],[GeneMolecularActivityRelationship]<gene_functions%200..*-++[GoCamAnnotations],[MolecularActivity]<activities%200..*-%20[GoCamAnnotations],[GeneOrganismRelationship]<gene_organisms%200..*-++[GoCamAnnotations],[Organism]<organisms%200..*-%20[GoCamAnnotations],[Gene]<genes%200..*-%20[GoCamAnnotations],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship],[GeneGeneInteraction],[Gene],[CellularProcess]) - -## Attributes - - -### Own - - * [➞genes](goCamAnnotations__genes.md) <sub>0..\*</sub> - * Description: semicolon-separated list of genes - * Range: [Gene](Gene.md) - * [➞organisms](goCamAnnotations__organisms.md) <sub>0..\*</sub> - * Description: semicolon-separated list of organism taxons - * Range: [Organism](Organism.md) - * [➞gene_organisms](goCamAnnotations__gene_organisms.md) <sub>0..\*</sub> - * Range: [GeneOrganismRelationship](GeneOrganismRelationship.md) - * [➞activities](goCamAnnotations__activities.md) <sub>0..\*</sub> - * Description: semicolon-separated list of molecular activities - * Range: [MolecularActivity](MolecularActivity.md) - * [➞gene_functions](goCamAnnotations__gene_functions.md) <sub>0..\*</sub> - * Description: semicolon-separated list of gene to molecular activity relationships - * Range: [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - * [➞cellular_processes](goCamAnnotations__cellular_processes.md) <sub>0..\*</sub> - * Description: semicolon-separated list of cellular processes - * Range: [CellularProcess](CellularProcess.md) - * [➞pathways](goCamAnnotations__pathways.md) <sub>0..\*</sub> - * Description: semicolon-separated list of pathways - * Range: [Pathway](Pathway.md) - * [➞gene_gene_interactions](goCamAnnotations__gene_gene_interactions.md) <sub>0..\*</sub> - * Description: semicolon-separated list of gene to gene interactions - * Range: [GeneGeneInteraction](GeneGeneInteraction.md) - * [➞gene_localizations](goCamAnnotations__gene_localizations.md) <sub>0..\*</sub> - * Description: semicolon-separated list of genes plus their location in the cell; for example, "gene1 / cytoplasm; gene2 / mitochondrion" - * Range: [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) diff --git a/projects/gocam/docs/MolecularActivity.md b/projects/gocam/docs/MolecularActivity.md deleted file mode 100644 index 2fa43b454..000000000 --- a/projects/gocam/docs/MolecularActivity.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: MolecularActivity - - - - -URI: [gocam:MolecularActivity](http://w3id.org/ontogpt/gocam/MolecularActivity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneMolecularActivityRelationship2]-%20molecular_activity%200..1>[MolecularActivity|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20molecular_activity%200..1>[MolecularActivity],[GoCamAnnotations]-%20activities%200..*>[MolecularActivity],[NamedEntity]^-[MolecularActivity],[GoCamAnnotations],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneMolecularActivityRelationship2]-%20molecular_activity%200..1>[MolecularActivity|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20molecular_activity%200..1>[MolecularActivity],[GoCamAnnotations]-%20activities%200..*>[MolecularActivity],[NamedEntity]^-[MolecularActivity],[GoCamAnnotations],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship]) - -## Identifier prefixes - - * GO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞molecular_activity](geneMolecularActivityRelationship2__molecular_activity.md)* <sub>0..1</sub> **[MolecularActivity](MolecularActivity.md)** - * **None** *[➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md)* <sub>0..1</sub> **[MolecularActivity](MolecularActivity.md)** - * **None** *[➞activities](goCamAnnotations__activities.md)* <sub>0..\*</sub> **[MolecularActivity](MolecularActivity.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/Molecule.md b/projects/gocam/docs/Molecule.md deleted file mode 100644 index 2dc4c84f4..000000000 --- a/projects/gocam/docs/Molecule.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Molecule - - - - -URI: [gocam:Molecule](http://w3id.org/ontogpt/gocam/Molecule) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneMolecularActivityRelationship2]-%20target%200..1>[Molecule|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Molecule],[GeneMolecularActivityRelationship2])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneMolecularActivityRelationship2]-%20target%200..1>[Molecule|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Molecule],[GeneMolecularActivityRelationship2]) - -## Identifier prefixes - - * CHEBI - * PR - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞target](geneMolecularActivityRelationship2__target.md)* <sub>0..1</sub> **[Molecule](Molecule.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/NamedEntity.md b/projects/gocam/docs/NamedEntity.md deleted file mode 100644 index 3896f74ca..000000000 --- a/projects/gocam/docs/NamedEntity.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [gocam:NamedEntity](http://w3id.org/ontogpt/gocam/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Pathway],[Organism],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Pathway],[NamedEntity]^-[Organism],[NamedEntity]^-[Molecule],[NamedEntity]^-[MolecularActivity],[NamedEntity]^-[GeneLocation],[NamedEntity]^-[Gene],[NamedEntity]^-[CellularProcess],[Triple],[Molecule],[MolecularActivity],[GeneLocation],[Gene],[CellularProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Pathway],[Organism],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Pathway],[NamedEntity]^-[Organism],[NamedEntity]^-[Molecule],[NamedEntity]^-[MolecularActivity],[NamedEntity]^-[GeneLocation],[NamedEntity]^-[Gene],[NamedEntity]^-[CellularProcess],[Triple],[Molecule],[MolecularActivity],[GeneLocation],[Gene],[CellularProcess]) - -## Children - - * [CellularProcess](CellularProcess.md) - * [Gene](Gene.md) - * [GeneLocation](GeneLocation.md) - * [MolecularActivity](MolecularActivity.md) - * [Molecule](Molecule.md) - * [Organism](Organism.md) - * [Pathway](Pathway.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/NullDataOptions.md b/projects/gocam/docs/NullDataOptions.md deleted file mode 100644 index abbb7e68a..000000000 --- a/projects/gocam/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [gocam:NullDataOptions](http://w3id.org/ontogpt/gocam/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/gocam/docs/Organism.md b/projects/gocam/docs/Organism.md deleted file mode 100644 index 9eb2f72e8..000000000 --- a/projects/gocam/docs/Organism.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: Organism - - - - -URI: [gocam:Organism](http://w3id.org/ontogpt/gocam/Organism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneOrganismRelationship]-%20organism%200..1>[Organism|id(i):string;label(i):string%20%3F],[GoCamAnnotations]-%20organisms%200..*>[Organism],[NamedEntity]^-[Organism],[NamedEntity],[GoCamAnnotations],[GeneOrganismRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneOrganismRelationship]-%20organism%200..1>[Organism|id(i):string;label(i):string%20%3F],[GoCamAnnotations]-%20organisms%200..*>[Organism],[NamedEntity]^-[Organism],[NamedEntity],[GoCamAnnotations],[GeneOrganismRelationship]) - -## Identifier prefixes - - * NCBITaxon - * EFO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞organism](geneOrganismRelationship__organism.md)* <sub>0..1</sub> **[Organism](Organism.md)** - * **None** *[➞organisms](goCamAnnotations__organisms.md)* <sub>0..\*</sub> **[Organism](Organism.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/Pathway.md b/projects/gocam/docs/Pathway.md deleted file mode 100644 index d64e098ef..000000000 --- a/projects/gocam/docs/Pathway.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Pathway - - - - -URI: [gocam:Pathway](http://w3id.org/ontogpt/gocam/Pathway) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[GoCamAnnotations]-%20pathways%200..*>[Pathway|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Pathway],[NamedEntity],[GoCamAnnotations])](https://yuml.me/diagram/nofunky;dir:TB/class/[GoCamAnnotations]-%20pathways%200..*>[Pathway|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Pathway],[NamedEntity],[GoCamAnnotations]) - -## Identifier prefixes - - * GO - * PW - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞pathways](goCamAnnotations__pathways.md)* <sub>0..\*</sub> **[Pathway](Pathway.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/Publication.md b/projects/gocam/docs/Publication.md deleted file mode 100644 index 64d87f10d..000000000 --- a/projects/gocam/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [gocam:Publication](http://w3id.org/ontogpt/gocam/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/RelationshipType.md b/projects/gocam/docs/RelationshipType.md deleted file mode 100644 index ea382170c..000000000 --- a/projects/gocam/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [gocam:RelationshipType](http://w3id.org/ontogpt/gocam/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/gocam/docs/TextWithTriples.md b/projects/gocam/docs/TextWithTriples.md deleted file mode 100644 index 77200b9c3..000000000 --- a/projects/gocam/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [gocam:TextWithTriples](http://w3id.org/ontogpt/gocam/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/gocam/docs/Triple.md b/projects/gocam/docs/Triple.md deleted file mode 100644 index 77c3e9483..000000000 --- a/projects/gocam/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [gocam:Triple](http://w3id.org/ontogpt/gocam/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/gocam/docs/annotatorResult__object_id.md b/projects/gocam/docs/annotatorResult__object_id.md deleted file mode 100644 index 77a3040ba..000000000 --- a/projects/gocam/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [gocam:annotatorResult__object_id](http://w3id.org/ontogpt/gocam/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/gocam/docs/annotatorResult__object_text.md b/projects/gocam/docs/annotatorResult__object_text.md deleted file mode 100644 index 2869435f2..000000000 --- a/projects/gocam/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [gocam:annotatorResult__object_text](http://w3id.org/ontogpt/gocam/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/gocam/docs/annotatorResult__subject_text.md b/projects/gocam/docs/annotatorResult__subject_text.md deleted file mode 100644 index 6f92b2c48..000000000 --- a/projects/gocam/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [gocam:annotatorResult__subject_text](http://w3id.org/ontogpt/gocam/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/gocam/docs/extractionResult__extracted_object.md b/projects/gocam/docs/extractionResult__extracted_object.md deleted file mode 100644 index 8e46f1540..000000000 --- a/projects/gocam/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [gocam:extractionResult__extracted_object](http://w3id.org/ontogpt/gocam/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gocam/docs/extractionResult__input_id.md b/projects/gocam/docs/extractionResult__input_id.md deleted file mode 100644 index d667d9cc3..000000000 --- a/projects/gocam/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [gocam:extractionResult__input_id](http://w3id.org/ontogpt/gocam/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gocam/docs/extractionResult__input_text.md b/projects/gocam/docs/extractionResult__input_text.md deleted file mode 100644 index 5d130aab5..000000000 --- a/projects/gocam/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [gocam:extractionResult__input_text](http://w3id.org/ontogpt/gocam/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gocam/docs/extractionResult__input_title.md b/projects/gocam/docs/extractionResult__input_title.md deleted file mode 100644 index 80c0a0585..000000000 --- a/projects/gocam/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [gocam:extractionResult__input_title](http://w3id.org/ontogpt/gocam/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gocam/docs/extractionResult__named_entities.md b/projects/gocam/docs/extractionResult__named_entities.md deleted file mode 100644 index 6680295e3..000000000 --- a/projects/gocam/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [gocam:extractionResult__named_entities](http://w3id.org/ontogpt/gocam/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gocam/docs/extractionResult__prompt.md b/projects/gocam/docs/extractionResult__prompt.md deleted file mode 100644 index 0bc5b4d86..000000000 --- a/projects/gocam/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [gocam:extractionResult__prompt](http://w3id.org/ontogpt/gocam/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gocam/docs/extractionResult__raw_completion_output.md b/projects/gocam/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index d5b8ad15b..000000000 --- a/projects/gocam/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [gocam:extractionResult__raw_completion_output](http://w3id.org/ontogpt/gocam/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/gocam/docs/geneGeneInteraction__gene1.md b/projects/gocam/docs/geneGeneInteraction__gene1.md deleted file mode 100644 index 25ff5d3e1..000000000 --- a/projects/gocam/docs/geneGeneInteraction__gene1.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene1 - - - - -URI: [gocam:geneGeneInteraction__gene1](http://w3id.org/ontogpt/gocam/geneGeneInteraction__gene1) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneGeneInteraction](GeneGeneInteraction.md) diff --git a/projects/gocam/docs/geneGeneInteraction__gene2.md b/projects/gocam/docs/geneGeneInteraction__gene2.md deleted file mode 100644 index 8ad830681..000000000 --- a/projects/gocam/docs/geneGeneInteraction__gene2.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene2 - - - - -URI: [gocam:geneGeneInteraction__gene2](http://w3id.org/ontogpt/gocam/geneGeneInteraction__gene2) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneGeneInteraction](GeneGeneInteraction.md) diff --git a/projects/gocam/docs/geneMolecularActivityRelationship2__gene.md b/projects/gocam/docs/geneMolecularActivityRelationship2__gene.md deleted file mode 100644 index 29e3876af..000000000 --- a/projects/gocam/docs/geneMolecularActivityRelationship2__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [gocam:geneMolecularActivityRelationship2__gene](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship2__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) diff --git a/projects/gocam/docs/geneMolecularActivityRelationship2__molecular_activity.md b/projects/gocam/docs/geneMolecularActivityRelationship2__molecular_activity.md deleted file mode 100644 index db47a4345..000000000 --- a/projects/gocam/docs/geneMolecularActivityRelationship2__molecular_activity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: molecular_activity - - - - -URI: [gocam:geneMolecularActivityRelationship2__molecular_activity](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship2__molecular_activity) - - -## Domain and Range - -None → <sub>0..1</sub> [MolecularActivity](MolecularActivity.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) diff --git a/projects/gocam/docs/geneMolecularActivityRelationship2__target.md b/projects/gocam/docs/geneMolecularActivityRelationship2__target.md deleted file mode 100644 index bb68d8cef..000000000 --- a/projects/gocam/docs/geneMolecularActivityRelationship2__target.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: target - - - - -URI: [gocam:geneMolecularActivityRelationship2__target](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship2__target) - - -## Domain and Range - -None → <sub>0..1</sub> [Molecule](Molecule.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) diff --git a/projects/gocam/docs/geneMolecularActivityRelationship__gene.md b/projects/gocam/docs/geneMolecularActivityRelationship__gene.md deleted file mode 100644 index e4df4fa20..000000000 --- a/projects/gocam/docs/geneMolecularActivityRelationship__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [gocam:geneMolecularActivityRelationship__gene](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) diff --git a/projects/gocam/docs/geneMolecularActivityRelationship__molecular_activity.md b/projects/gocam/docs/geneMolecularActivityRelationship__molecular_activity.md deleted file mode 100644 index 42577e0a6..000000000 --- a/projects/gocam/docs/geneMolecularActivityRelationship__molecular_activity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: molecular_activity - - - - -URI: [gocam:geneMolecularActivityRelationship__molecular_activity](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship__molecular_activity) - - -## Domain and Range - -None → <sub>0..1</sub> [MolecularActivity](MolecularActivity.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) diff --git a/projects/gocam/docs/geneOrganismRelationship__gene.md b/projects/gocam/docs/geneOrganismRelationship__gene.md deleted file mode 100644 index 7071e06cd..000000000 --- a/projects/gocam/docs/geneOrganismRelationship__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [gocam:geneOrganismRelationship__gene](http://w3id.org/ontogpt/gocam/geneOrganismRelationship__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneOrganismRelationship](GeneOrganismRelationship.md) diff --git a/projects/gocam/docs/geneOrganismRelationship__organism.md b/projects/gocam/docs/geneOrganismRelationship__organism.md deleted file mode 100644 index 80ad6c95a..000000000 --- a/projects/gocam/docs/geneOrganismRelationship__organism.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: organism - - - - -URI: [gocam:geneOrganismRelationship__organism](http://w3id.org/ontogpt/gocam/geneOrganismRelationship__organism) - - -## Domain and Range - -None → <sub>0..1</sub> [Organism](Organism.md) - -## Parents - - -## Children - - -## Used by - - * [GeneOrganismRelationship](GeneOrganismRelationship.md) diff --git a/projects/gocam/docs/geneSubcellularLocalizationRelationship__gene.md b/projects/gocam/docs/geneSubcellularLocalizationRelationship__gene.md deleted file mode 100644 index 719048841..000000000 --- a/projects/gocam/docs/geneSubcellularLocalizationRelationship__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [gocam:geneSubcellularLocalizationRelationship__gene](http://w3id.org/ontogpt/gocam/geneSubcellularLocalizationRelationship__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) diff --git a/projects/gocam/docs/geneSubcellularLocalizationRelationship__location.md b/projects/gocam/docs/geneSubcellularLocalizationRelationship__location.md deleted file mode 100644 index c5e53c56a..000000000 --- a/projects/gocam/docs/geneSubcellularLocalizationRelationship__location.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: location - - - - -URI: [gocam:geneSubcellularLocalizationRelationship__location](http://w3id.org/ontogpt/gocam/geneSubcellularLocalizationRelationship__location) - - -## Domain and Range - -None → <sub>0..1</sub> [GeneLocation](GeneLocation.md) - -## Parents - - -## Children - - -## Used by - - * [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) diff --git a/projects/gocam/docs/goCamAnnotations__activities.md b/projects/gocam/docs/goCamAnnotations__activities.md deleted file mode 100644 index bf256fa2a..000000000 --- a/projects/gocam/docs/goCamAnnotations__activities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: activities - - -semicolon-separated list of molecular activities - -URI: [gocam:goCamAnnotations__activities](http://w3id.org/ontogpt/gocam/goCamAnnotations__activities) - - -## Domain and Range - -None → <sub>0..\*</sub> [MolecularActivity](MolecularActivity.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/goCamAnnotations__cellular_processes.md b/projects/gocam/docs/goCamAnnotations__cellular_processes.md deleted file mode 100644 index bdd8d8787..000000000 --- a/projects/gocam/docs/goCamAnnotations__cellular_processes.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: cellular_processes - - -semicolon-separated list of cellular processes - -URI: [gocam:goCamAnnotations__cellular_processes](http://w3id.org/ontogpt/gocam/goCamAnnotations__cellular_processes) - - -## Domain and Range - -None → <sub>0..\*</sub> [CellularProcess](CellularProcess.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/goCamAnnotations__gene_functions.md b/projects/gocam/docs/goCamAnnotations__gene_functions.md deleted file mode 100644 index 47da49890..000000000 --- a/projects/gocam/docs/goCamAnnotations__gene_functions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_functions - - -semicolon-separated list of gene to molecular activity relationships - -URI: [gocam:goCamAnnotations__gene_functions](http://w3id.org/ontogpt/gocam/goCamAnnotations__gene_functions) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/goCamAnnotations__gene_gene_interactions.md b/projects/gocam/docs/goCamAnnotations__gene_gene_interactions.md deleted file mode 100644 index 5eb3bea2e..000000000 --- a/projects/gocam/docs/goCamAnnotations__gene_gene_interactions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_gene_interactions - - -semicolon-separated list of gene to gene interactions - -URI: [gocam:goCamAnnotations__gene_gene_interactions](http://w3id.org/ontogpt/gocam/goCamAnnotations__gene_gene_interactions) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneGeneInteraction](GeneGeneInteraction.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/goCamAnnotations__gene_localizations.md b/projects/gocam/docs/goCamAnnotations__gene_localizations.md deleted file mode 100644 index 6815039e0..000000000 --- a/projects/gocam/docs/goCamAnnotations__gene_localizations.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_localizations - - -semicolon-separated list of genes plus their location in the cell; for example, "gene1 / cytoplasm; gene2 / mitochondrion" - -URI: [gocam:goCamAnnotations__gene_localizations](http://w3id.org/ontogpt/gocam/goCamAnnotations__gene_localizations) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/goCamAnnotations__gene_organisms.md b/projects/gocam/docs/goCamAnnotations__gene_organisms.md deleted file mode 100644 index 946e06471..000000000 --- a/projects/gocam/docs/goCamAnnotations__gene_organisms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_organisms - - - - -URI: [gocam:goCamAnnotations__gene_organisms](http://w3id.org/ontogpt/gocam/goCamAnnotations__gene_organisms) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneOrganismRelationship](GeneOrganismRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/goCamAnnotations__genes.md b/projects/gocam/docs/goCamAnnotations__genes.md deleted file mode 100644 index c505077b7..000000000 --- a/projects/gocam/docs/goCamAnnotations__genes.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: genes - - -semicolon-separated list of genes - -URI: [gocam:goCamAnnotations__genes](http://w3id.org/ontogpt/gocam/goCamAnnotations__genes) - - -## Domain and Range - -None → <sub>0..\*</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/goCamAnnotations__organisms.md b/projects/gocam/docs/goCamAnnotations__organisms.md deleted file mode 100644 index 9e4d3b2d5..000000000 --- a/projects/gocam/docs/goCamAnnotations__organisms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: organisms - - -semicolon-separated list of organism taxons - -URI: [gocam:goCamAnnotations__organisms](http://w3id.org/ontogpt/gocam/goCamAnnotations__organisms) - - -## Domain and Range - -None → <sub>0..\*</sub> [Organism](Organism.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/goCamAnnotations__pathways.md b/projects/gocam/docs/goCamAnnotations__pathways.md deleted file mode 100644 index 5c47b4bda..000000000 --- a/projects/gocam/docs/goCamAnnotations__pathways.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: pathways - - -semicolon-separated list of pathways - -URI: [gocam:goCamAnnotations__pathways](http://w3id.org/ontogpt/gocam/goCamAnnotations__pathways) - - -## Domain and Range - -None → <sub>0..\*</sub> [Pathway](Pathway.md) - -## Parents - - -## Children - - -## Used by - - * [GoCamAnnotations](GoCamAnnotations.md) diff --git a/projects/gocam/docs/gocam.md b/projects/gocam/docs/gocam.md deleted file mode 100644 index b13277173..000000000 --- a/projects/gocam/docs/gocam.md +++ /dev/null @@ -1,140 +0,0 @@ - -# gocam-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for GO-CAMs - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [GeneGeneInteraction](GeneGeneInteraction.md) - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) - * [GeneOrganismRelationship](GeneOrganismRelationship.md) - * [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [GoCamAnnotations](GoCamAnnotations.md) - * [NamedEntity](NamedEntity.md) - * [CellularProcess](CellularProcess.md) - * [Gene](Gene.md) - * [GeneLocation](GeneLocation.md) - * [MolecularActivity](MolecularActivity.md) - * [Molecule](Molecule.md) - * [Organism](Organism.md) - * [Pathway](Pathway.md) - * [RelationshipType](RelationshipType.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞gene1](geneGeneInteraction__gene1.md) - * [➞gene2](geneGeneInteraction__gene2.md) - * [➞gene](geneMolecularActivityRelationship2__gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship2__molecular_activity.md) - * [➞target](geneMolecularActivityRelationship2__target.md) - * [➞gene](geneMolecularActivityRelationship__gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md) - * [➞gene](geneOrganismRelationship__gene.md) - * [➞organism](geneOrganismRelationship__organism.md) - * [➞gene](geneSubcellularLocalizationRelationship__gene.md) - * [➞location](geneSubcellularLocalizationRelationship__location.md) - * [➞activities](goCamAnnotations__activities.md) - semicolon-separated list of molecular activities - * [➞cellular_processes](goCamAnnotations__cellular_processes.md) - semicolon-separated list of cellular processes - * [➞gene_functions](goCamAnnotations__gene_functions.md) - semicolon-separated list of gene to molecular activity relationships - * [➞gene_gene_interactions](goCamAnnotations__gene_gene_interactions.md) - semicolon-separated list of gene to gene interactions - * [➞gene_localizations](goCamAnnotations__gene_localizations.md) - semicolon-separated list of genes plus their location in the cell; for example, "gene1 / cytoplasm; gene2 / mitochondrion" - * [➞gene_organisms](goCamAnnotations__gene_organisms.md) - * [➞genes](goCamAnnotations__genes.md) - semicolon-separated list of genes - * [➞organisms](goCamAnnotations__organisms.md) - semicolon-separated list of organism taxons - * [➞pathways](goCamAnnotations__pathways.md) - semicolon-separated list of pathways - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [GeneLocation➞id](GeneLocation_id.md) - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [CellType](CellType.md) - * [GOCellComponentType](GOCellComponentType.md) - * [GeneLocationEnum](GeneLocationEnum.md) - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/gocam/docs/namedEntity__id.md b/projects/gocam/docs/namedEntity__id.md deleted file mode 100644 index 0555a9f73..000000000 --- a/projects/gocam/docs/namedEntity__id.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [gocam:namedEntity__id](http://w3id.org/ontogpt/gocam/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - * [GeneLocation➞id](GeneLocation_id.md) - -## Used by - - * [CellularProcess](CellularProcess.md) - * [Gene](Gene.md) - * [MolecularActivity](MolecularActivity.md) - * [Molecule](Molecule.md) - * [NamedEntity](NamedEntity.md) - * [Organism](Organism.md) - * [Pathway](Pathway.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/gocam/docs/namedEntity__label.md b/projects/gocam/docs/namedEntity__label.md deleted file mode 100644 index 2b599b1cc..000000000 --- a/projects/gocam/docs/namedEntity__label.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [gocam:namedEntity__label](http://w3id.org/ontogpt/gocam/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [CellularProcess](CellularProcess.md) - * [Gene](Gene.md) - * [GeneLocation](GeneLocation.md) - * [MolecularActivity](MolecularActivity.md) - * [Molecule](Molecule.md) - * [NamedEntity](NamedEntity.md) - * [Organism](Organism.md) - * [Pathway](Pathway.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/gocam/docs/publication__abstract.md b/projects/gocam/docs/publication__abstract.md deleted file mode 100644 index dd434bed1..000000000 --- a/projects/gocam/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [gocam:publication__abstract](http://w3id.org/ontogpt/gocam/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gocam/docs/publication__combined_text.md b/projects/gocam/docs/publication__combined_text.md deleted file mode 100644 index 128ca7aed..000000000 --- a/projects/gocam/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [gocam:publication__combined_text](http://w3id.org/ontogpt/gocam/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gocam/docs/publication__full_text.md b/projects/gocam/docs/publication__full_text.md deleted file mode 100644 index be255126c..000000000 --- a/projects/gocam/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [gocam:publication__full_text](http://w3id.org/ontogpt/gocam/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gocam/docs/publication__id.md b/projects/gocam/docs/publication__id.md deleted file mode 100644 index 583585698..000000000 --- a/projects/gocam/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [gocam:publication__id](http://w3id.org/ontogpt/gocam/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gocam/docs/publication__title.md b/projects/gocam/docs/publication__title.md deleted file mode 100644 index af7b52d3f..000000000 --- a/projects/gocam/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [gocam:publication__title](http://w3id.org/ontogpt/gocam/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/gocam/docs/textWithTriples__publication.md b/projects/gocam/docs/textWithTriples__publication.md deleted file mode 100644 index f2480d2c2..000000000 --- a/projects/gocam/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [gocam:textWithTriples__publication](http://w3id.org/ontogpt/gocam/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/gocam/docs/textWithTriples__triples.md b/projects/gocam/docs/textWithTriples__triples.md deleted file mode 100644 index 8fe102100..000000000 --- a/projects/gocam/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [gocam:textWithTriples__triples](http://w3id.org/ontogpt/gocam/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/gocam/docs/triple__object.md b/projects/gocam/docs/triple__object.md deleted file mode 100644 index 38e4c4c25..000000000 --- a/projects/gocam/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [gocam:triple__object](http://w3id.org/ontogpt/gocam/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gocam/docs/triple__object_qualifier.md b/projects/gocam/docs/triple__object_qualifier.md deleted file mode 100644 index 21bae818d..000000000 --- a/projects/gocam/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [gocam:triple__object_qualifier](http://w3id.org/ontogpt/gocam/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gocam/docs/triple__predicate.md b/projects/gocam/docs/triple__predicate.md deleted file mode 100644 index 3c7c729c3..000000000 --- a/projects/gocam/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [gocam:triple__predicate](http://w3id.org/ontogpt/gocam/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gocam/docs/triple__qualifier.md b/projects/gocam/docs/triple__qualifier.md deleted file mode 100644 index 7f62d89e8..000000000 --- a/projects/gocam/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [gocam:triple__qualifier](http://w3id.org/ontogpt/gocam/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gocam/docs/triple__subject.md b/projects/gocam/docs/triple__subject.md deleted file mode 100644 index 9b9ece18a..000000000 --- a/projects/gocam/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [gocam:triple__subject](http://w3id.org/ontogpt/gocam/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gocam/docs/triple__subject_qualifier.md b/projects/gocam/docs/triple__subject_qualifier.md deleted file mode 100644 index 588c54157..000000000 --- a/projects/gocam/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [gocam:triple__subject_qualifier](http://w3id.org/ontogpt/gocam/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/gocam/docs/types/Boolean.md b/projects/gocam/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/gocam/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/gocam/docs/types/Curie.md b/projects/gocam/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/gocam/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/gocam/docs/types/Date.md b/projects/gocam/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/gocam/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/gocam/docs/types/DateOrDatetime.md b/projects/gocam/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/gocam/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/gocam/docs/types/Datetime.md b/projects/gocam/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/gocam/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/gocam/docs/types/Decimal.md b/projects/gocam/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/gocam/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/gocam/docs/types/Double.md b/projects/gocam/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/gocam/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/gocam/docs/types/Float.md b/projects/gocam/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/gocam/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/gocam/docs/types/Integer.md b/projects/gocam/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/gocam/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/gocam/docs/types/Jsonpath.md b/projects/gocam/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/gocam/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/gocam/docs/types/Jsonpointer.md b/projects/gocam/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/gocam/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/gocam/docs/types/Ncname.md b/projects/gocam/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/gocam/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/gocam/docs/types/Nodeidentifier.md b/projects/gocam/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/gocam/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/gocam/docs/types/Objectidentifier.md b/projects/gocam/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/gocam/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/gocam/docs/types/Sparqlpath.md b/projects/gocam/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/gocam/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/gocam/docs/types/String.md b/projects/gocam/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/gocam/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/gocam/docs/types/Time.md b/projects/gocam/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/gocam/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/gocam/docs/types/Uri.md b/projects/gocam/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/gocam/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/gocam/docs/types/Uriorcurie.md b/projects/gocam/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/gocam/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/gocam/excel/gocam.xlsx b/projects/gocam/excel/gocam.xlsx deleted file mode 100644 index c51f66c3a802ae3f6f7a92c1289fa7bc39212e9b..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 13541 zcmeHObyO7EzNWiV8YBfoI;6WKq`P4N=|;M{OKGILyBnlKkZwUhDd~Cx-g7<jIQN}@ z-n##sVa?29E%wKr@7LenBP$6GfdK*n0s~U71g$Kh){fu}{H+}LL;*exEcIn=EUj!` z=vrCPIhmVDg-gMA(4z?5N_<_gP~0bGAfC)z?spMmV~sQrbnv@!m2Z!j<65K-ZNU7f 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index ee7727d40..000000000 --- a/projects/gocam/gocam.py +++ /dev/null @@ -1,794 +0,0 @@ -# Auto generated from gocam.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:53:47 -# Schema: gocam-template -# -# id: http://w3id.org/ontogpt/gocam -# description: A template for GO-CAMs -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CHEBI = CurieNamespace('CHEBI', 'http://example.org/UNKNOWN/CHEBI/') -CL = CurieNamespace('CL', 'http://purl.obolibrary.org/obo/CL_') -EFO = CurieNamespace('EFO', 'http://example.org/UNKNOWN/EFO/') -GO = CurieNamespace('GO', 'http://purl.obolibrary.org/obo/GO_') -HGNC = CurieNamespace('HGNC', 'http://example.org/UNKNOWN/HGNC/') -NCBITAXON = CurieNamespace('NCBITaxon', 'http://example.org/UNKNOWN/NCBITaxon/') -PR = CurieNamespace('PR', 'http://example.org/UNKNOWN/PR/') -PW = CurieNamespace('PW', 'http://example.org/UNKNOWN/PW/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -UBERON = CurieNamespace('UBERON', 'http://example.org/UNKNOWN/UBERON/') -UNIPROTKB = CurieNamespace('UniProtKB', 'http://example.org/UNKNOWN/UniProtKB/') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -GOCAM = CurieNamespace('gocam', 'http://w3id.org/ontogpt/gocam/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = GOCAM - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class GeneId(NamedEntityId): - pass - - -class PathwayId(NamedEntityId): - pass - - -class CellularProcessId(NamedEntityId): - pass - - -class MolecularActivityId(NamedEntityId): - pass - - -class GeneLocationId(NamedEntityId): - pass - - -class OrganismId(NamedEntityId): - pass - - -class MoleculeId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class GoCamAnnotations(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GoCamAnnotations - class_class_curie: ClassVar[str] = "gocam:GoCamAnnotations" - class_name: ClassVar[str] = "GoCamAnnotations" - class_model_uri: ClassVar[URIRef] = GOCAM.GoCamAnnotations - - genes: Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]] = empty_list() - organisms: Optional[Union[Union[str, OrganismId], List[Union[str, OrganismId]]]] = empty_list() - gene_organisms: Optional[Union[Union[dict, "GeneOrganismRelationship"], List[Union[dict, "GeneOrganismRelationship"]]]] = empty_list() - activities: Optional[Union[Union[str, MolecularActivityId], List[Union[str, MolecularActivityId]]]] = empty_list() - gene_functions: Optional[Union[Union[dict, "GeneMolecularActivityRelationship"], List[Union[dict, "GeneMolecularActivityRelationship"]]]] = empty_list() - cellular_processes: Optional[Union[Union[str, CellularProcessId], List[Union[str, CellularProcessId]]]] = empty_list() - pathways: Optional[Union[Union[str, PathwayId], List[Union[str, PathwayId]]]] = empty_list() - gene_gene_interactions: Optional[Union[Union[dict, "GeneGeneInteraction"], List[Union[dict, "GeneGeneInteraction"]]]] = empty_list() - gene_localizations: Optional[Union[Union[dict, "GeneSubcellularLocalizationRelationship"], List[Union[dict, "GeneSubcellularLocalizationRelationship"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.genes, list): - self.genes = [self.genes] if self.genes is not None else [] - self.genes = [v if isinstance(v, GeneId) else GeneId(v) for v in self.genes] - - if not isinstance(self.organisms, list): - self.organisms = [self.organisms] if self.organisms is not None else [] - self.organisms = [v if isinstance(v, OrganismId) else OrganismId(v) for v in self.organisms] - - if not isinstance(self.gene_organisms, list): - self.gene_organisms = [self.gene_organisms] if self.gene_organisms is not None else [] - self.gene_organisms = [v if isinstance(v, GeneOrganismRelationship) else GeneOrganismRelationship(**as_dict(v)) for v in self.gene_organisms] - - if not isinstance(self.activities, list): - self.activities = [self.activities] if self.activities is not None else [] - self.activities = [v if isinstance(v, MolecularActivityId) else MolecularActivityId(v) for v in self.activities] - - if not isinstance(self.gene_functions, list): - self.gene_functions = [self.gene_functions] if self.gene_functions is not None else [] - self.gene_functions = [v if isinstance(v, GeneMolecularActivityRelationship) else GeneMolecularActivityRelationship(**as_dict(v)) for v in self.gene_functions] - - if not isinstance(self.cellular_processes, list): - self.cellular_processes = [self.cellular_processes] if self.cellular_processes is not None else [] - self.cellular_processes = [v if isinstance(v, CellularProcessId) else CellularProcessId(v) for v in self.cellular_processes] - - if not isinstance(self.pathways, list): - self.pathways = [self.pathways] if self.pathways is not None else [] - self.pathways = [v if isinstance(v, PathwayId) else PathwayId(v) for v in self.pathways] - - if not isinstance(self.gene_gene_interactions, list): - self.gene_gene_interactions = [self.gene_gene_interactions] if self.gene_gene_interactions is not None else [] - self.gene_gene_interactions = [v if isinstance(v, GeneGeneInteraction) else GeneGeneInteraction(**as_dict(v)) for v in self.gene_gene_interactions] - - if not isinstance(self.gene_localizations, list): - self.gene_localizations = [self.gene_localizations] if self.gene_localizations is not None else [] - self.gene_localizations = [v if isinstance(v, GeneSubcellularLocalizationRelationship) else GeneSubcellularLocalizationRelationship(**as_dict(v)) for v in self.gene_localizations] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = GOCAM.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = GOCAM.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.Gene - class_class_curie: ClassVar[str] = "gocam:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = GOCAM.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Pathway(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.Pathway - class_class_curie: ClassVar[str] = "gocam:Pathway" - class_name: ClassVar[str] = "Pathway" - class_model_uri: ClassVar[URIRef] = GOCAM.Pathway - - id: Union[str, PathwayId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PathwayId): - self.id = PathwayId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class CellularProcess(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.CellularProcess - class_class_curie: ClassVar[str] = "gocam:CellularProcess" - class_name: ClassVar[str] = "CellularProcess" - class_model_uri: ClassVar[URIRef] = GOCAM.CellularProcess - - id: Union[str, CellularProcessId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, CellularProcessId): - self.id = CellularProcessId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class MolecularActivity(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.MolecularActivity - class_class_curie: ClassVar[str] = "gocam:MolecularActivity" - class_name: ClassVar[str] = "MolecularActivity" - class_model_uri: ClassVar[URIRef] = GOCAM.MolecularActivity - - id: Union[str, MolecularActivityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MolecularActivityId): - self.id = MolecularActivityId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneLocation(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneLocation - class_class_curie: ClassVar[str] = "gocam:GeneLocation" - class_name: ClassVar[str] = "GeneLocation" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneLocation - - id: Union[str, GeneLocationId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneLocationId): - self.id = GeneLocationId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Organism(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.Organism - class_class_curie: ClassVar[str] = "gocam:Organism" - class_name: ClassVar[str] = "Organism" - class_model_uri: ClassVar[URIRef] = GOCAM.Organism - - id: Union[str, OrganismId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OrganismId): - self.id = OrganismId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Molecule(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.Molecule - class_class_curie: ClassVar[str] = "gocam:Molecule" - class_name: ClassVar[str] = "Molecule" - class_model_uri: ClassVar[URIRef] = GOCAM.Molecule - - id: Union[str, MoleculeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MoleculeId): - self.id = MoleculeId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = GOCAM.CompoundExpression - - -@dataclass -class GeneOrganismRelationship(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneOrganismRelationship - class_class_curie: ClassVar[str] = "gocam:GeneOrganismRelationship" - class_name: ClassVar[str] = "GeneOrganismRelationship" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneOrganismRelationship - - gene: Optional[Union[str, GeneId]] = None - organism: Optional[Union[str, OrganismId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.organism is not None and not isinstance(self.organism, OrganismId): - self.organism = OrganismId(self.organism) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneMolecularActivityRelationship(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneMolecularActivityRelationship - class_class_curie: ClassVar[str] = "gocam:GeneMolecularActivityRelationship" - class_name: ClassVar[str] = "GeneMolecularActivityRelationship" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneMolecularActivityRelationship - - gene: Optional[Union[str, GeneId]] = None - molecular_activity: Optional[Union[str, MolecularActivityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.molecular_activity is not None and not isinstance(self.molecular_activity, MolecularActivityId): - self.molecular_activity = MolecularActivityId(self.molecular_activity) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneMolecularActivityRelationship2(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneMolecularActivityRelationship2 - class_class_curie: ClassVar[str] = "gocam:GeneMolecularActivityRelationship2" - class_name: ClassVar[str] = "GeneMolecularActivityRelationship2" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneMolecularActivityRelationship2 - - gene: Optional[Union[str, GeneId]] = None - molecular_activity: Optional[Union[str, MolecularActivityId]] = None - target: Optional[Union[str, MoleculeId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.molecular_activity is not None and not isinstance(self.molecular_activity, MolecularActivityId): - self.molecular_activity = MolecularActivityId(self.molecular_activity) - - if self.target is not None and not isinstance(self.target, MoleculeId): - self.target = MoleculeId(self.target) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneSubcellularLocalizationRelationship(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneSubcellularLocalizationRelationship - class_class_curie: ClassVar[str] = "gocam:GeneSubcellularLocalizationRelationship" - class_name: ClassVar[str] = "GeneSubcellularLocalizationRelationship" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneSubcellularLocalizationRelationship - - gene: Optional[Union[str, GeneId]] = None - location: Optional[Union[str, GeneLocationId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.location is not None and not isinstance(self.location, GeneLocationId): - self.location = GeneLocationId(self.location) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneGeneInteraction(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneGeneInteraction - class_class_curie: ClassVar[str] = "gocam:GeneGeneInteraction" - class_name: ClassVar[str] = "GeneGeneInteraction" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneGeneInteraction - - gene1: Optional[Union[str, GeneId]] = None - gene2: Optional[Union[str, GeneId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene1 is not None and not isinstance(self.gene1, GeneId): - self.gene1 = GeneId(self.gene1) - - if self.gene2 is not None and not isinstance(self.gene2, GeneId): - self.gene2 = GeneId(self.gene2) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = GOCAM.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = GOCAM.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = GOCAM.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = GOCAM.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = GOCAM.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class GeneLocationEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="GeneLocationEnum", - ) - -class GOCellComponentType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="GOCellComponentType", - ) - -class CellType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="CellType", - ) - -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.goCamAnnotations__genes = Slot(uri=GOCAM.genes, name="goCamAnnotations__genes", curie=GOCAM.curie('genes'), - model_uri=GOCAM.goCamAnnotations__genes, domain=None, range=Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]]) - -slots.goCamAnnotations__organisms = Slot(uri=GOCAM.organisms, name="goCamAnnotations__organisms", curie=GOCAM.curie('organisms'), - model_uri=GOCAM.goCamAnnotations__organisms, domain=None, range=Optional[Union[Union[str, OrganismId], List[Union[str, OrganismId]]]]) - -slots.goCamAnnotations__gene_organisms = Slot(uri=GOCAM.gene_organisms, name="goCamAnnotations__gene_organisms", curie=GOCAM.curie('gene_organisms'), - model_uri=GOCAM.goCamAnnotations__gene_organisms, domain=None, range=Optional[Union[Union[dict, GeneOrganismRelationship], List[Union[dict, GeneOrganismRelationship]]]]) - -slots.goCamAnnotations__activities = Slot(uri=GOCAM.activities, name="goCamAnnotations__activities", curie=GOCAM.curie('activities'), - model_uri=GOCAM.goCamAnnotations__activities, domain=None, range=Optional[Union[Union[str, MolecularActivityId], List[Union[str, MolecularActivityId]]]]) - -slots.goCamAnnotations__gene_functions = Slot(uri=GOCAM.gene_functions, name="goCamAnnotations__gene_functions", curie=GOCAM.curie('gene_functions'), - model_uri=GOCAM.goCamAnnotations__gene_functions, domain=None, range=Optional[Union[Union[dict, GeneMolecularActivityRelationship], List[Union[dict, GeneMolecularActivityRelationship]]]]) - -slots.goCamAnnotations__cellular_processes = Slot(uri=GOCAM.cellular_processes, name="goCamAnnotations__cellular_processes", curie=GOCAM.curie('cellular_processes'), - model_uri=GOCAM.goCamAnnotations__cellular_processes, domain=None, range=Optional[Union[Union[str, CellularProcessId], List[Union[str, CellularProcessId]]]]) - -slots.goCamAnnotations__pathways = Slot(uri=GOCAM.pathways, name="goCamAnnotations__pathways", curie=GOCAM.curie('pathways'), - model_uri=GOCAM.goCamAnnotations__pathways, domain=None, range=Optional[Union[Union[str, PathwayId], List[Union[str, PathwayId]]]]) - -slots.goCamAnnotations__gene_gene_interactions = Slot(uri=GOCAM.gene_gene_interactions, name="goCamAnnotations__gene_gene_interactions", curie=GOCAM.curie('gene_gene_interactions'), - model_uri=GOCAM.goCamAnnotations__gene_gene_interactions, domain=None, range=Optional[Union[Union[dict, GeneGeneInteraction], List[Union[dict, GeneGeneInteraction]]]]) - -slots.goCamAnnotations__gene_localizations = Slot(uri=GOCAM.gene_localizations, name="goCamAnnotations__gene_localizations", curie=GOCAM.curie('gene_localizations'), - model_uri=GOCAM.goCamAnnotations__gene_localizations, domain=None, range=Optional[Union[Union[dict, GeneSubcellularLocalizationRelationship], List[Union[dict, GeneSubcellularLocalizationRelationship]]]]) - -slots.geneOrganismRelationship__gene = Slot(uri=GOCAM.gene, name="geneOrganismRelationship__gene", curie=GOCAM.curie('gene'), - model_uri=GOCAM.geneOrganismRelationship__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneOrganismRelationship__organism = Slot(uri=GOCAM.organism, name="geneOrganismRelationship__organism", curie=GOCAM.curie('organism'), - model_uri=GOCAM.geneOrganismRelationship__organism, domain=None, range=Optional[Union[str, OrganismId]]) - -slots.geneMolecularActivityRelationship__gene = Slot(uri=GOCAM.gene, name="geneMolecularActivityRelationship__gene", curie=GOCAM.curie('gene'), - model_uri=GOCAM.geneMolecularActivityRelationship__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneMolecularActivityRelationship__molecular_activity = Slot(uri=GOCAM.molecular_activity, name="geneMolecularActivityRelationship__molecular_activity", curie=GOCAM.curie('molecular_activity'), - model_uri=GOCAM.geneMolecularActivityRelationship__molecular_activity, domain=None, range=Optional[Union[str, MolecularActivityId]]) - -slots.geneMolecularActivityRelationship2__gene = Slot(uri=GOCAM.gene, name="geneMolecularActivityRelationship2__gene", curie=GOCAM.curie('gene'), - model_uri=GOCAM.geneMolecularActivityRelationship2__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneMolecularActivityRelationship2__molecular_activity = Slot(uri=GOCAM.molecular_activity, name="geneMolecularActivityRelationship2__molecular_activity", curie=GOCAM.curie('molecular_activity'), - model_uri=GOCAM.geneMolecularActivityRelationship2__molecular_activity, domain=None, range=Optional[Union[str, MolecularActivityId]]) - -slots.geneMolecularActivityRelationship2__target = Slot(uri=GOCAM.target, name="geneMolecularActivityRelationship2__target", curie=GOCAM.curie('target'), - model_uri=GOCAM.geneMolecularActivityRelationship2__target, domain=None, range=Optional[Union[str, MoleculeId]]) - -slots.geneSubcellularLocalizationRelationship__gene = Slot(uri=GOCAM.gene, name="geneSubcellularLocalizationRelationship__gene", curie=GOCAM.curie('gene'), - model_uri=GOCAM.geneSubcellularLocalizationRelationship__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneSubcellularLocalizationRelationship__location = Slot(uri=GOCAM.location, name="geneSubcellularLocalizationRelationship__location", curie=GOCAM.curie('location'), - model_uri=GOCAM.geneSubcellularLocalizationRelationship__location, domain=None, range=Optional[Union[str, GeneLocationId]]) - -slots.geneGeneInteraction__gene1 = Slot(uri=GOCAM.gene1, name="geneGeneInteraction__gene1", curie=GOCAM.curie('gene1'), - model_uri=GOCAM.geneGeneInteraction__gene1, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneGeneInteraction__gene2 = Slot(uri=GOCAM.gene2, name="geneGeneInteraction__gene2", curie=GOCAM.curie('gene2'), - model_uri=GOCAM.geneGeneInteraction__gene2, domain=None, range=Optional[Union[str, GeneId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=GOCAM.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=GOCAM.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=GOCAM.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=GOCAM.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=GOCAM.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=GOCAM.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=GOCAM.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=GOCAM.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=GOCAM.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=GOCAM.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=GOCAM.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=GOCAM.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=GOCAM.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=GOCAM.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=GOCAM.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=GOCAM.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=GOCAM.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=GOCAM.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=GOCAM.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=GOCAM.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=GOCAM.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=GOCAM.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=GOCAM.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=GOCAM.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=GOCAM.annotatorResult__object_text, domain=None, range=Optional[str]) - -slots.GeneLocation_id = Slot(uri=GOCAM.id, name="GeneLocation_id", curie=GOCAM.curie('id'), - model_uri=GOCAM.GeneLocation_id, domain=GeneLocation, range=Union[str, GeneLocationId]) \ No newline at end of file diff --git a/projects/gocam/graphql/gocam.graphql b/projects/gocam/graphql/gocam.graphql deleted file mode 100644 index 56eed285d..000000000 --- a/projects/gocam/graphql/gocam.graphql +++ /dev/null @@ -1,149 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type CellularProcess - { - id: String! - label: String - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Gene - { - id: String! - label: String - } - -type GeneGeneInteraction - { - gene1: Gene - gene2: Gene - } - -type GeneLocation - { - label: String - id: String! - } - -type GeneMolecularActivityRelationship - { - gene: Gene - molecularActivity: MolecularActivity - } - -type GeneMolecularActivityRelationship2 - { - gene: Gene - molecularActivity: MolecularActivity - target: Molecule - } - -type GeneOrganismRelationship - { - gene: Gene - organism: Organism - } - -type GeneSubcellularLocalizationRelationship - { - gene: Gene - location: GeneLocation - } - -type GoCamAnnotations - { - genes: [Gene] - organisms: [Organism] - geneOrganisms: [GeneOrganismRelationship] - activities: [MolecularActivity] - geneFunctions: [GeneMolecularActivityRelationship] - cellularProcesses: [CellularProcess] - pathways: [Pathway] - geneGeneInteractions: [GeneGeneInteraction] - geneLocalizations: [GeneSubcellularLocalizationRelationship] - } - -type MolecularActivity - { - id: String! - label: String - } - -type Molecule - { - id: String! - label: String - } - -interface NamedEntity - { - id: String! - label: String - } - -type Organism - { - id: String! - label: String - } - -type Pathway - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/gocam/jsonld/gocam.context.jsonld b/projects/gocam/jsonld/gocam.context.jsonld deleted file mode 100644 index 400a8db89..000000000 --- a/projects/gocam/jsonld/gocam.context.jsonld +++ /dev/null @@ -1,191 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:53:36", - "source": "gocam.yaml" - }, - "@context": { - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "CL": { - "@id": "http://purl.obolibrary.org/obo/CL_", - "@prefix": true - }, - "EFO": "http://example.org/UNKNOWN/EFO/", - "GO": { - "@id": "http://purl.obolibrary.org/obo/GO_", - "@prefix": true - }, - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "NCBITaxon": "http://example.org/UNKNOWN/NCBITaxon/", - "PR": "http://example.org/UNKNOWN/PR/", - "PW": "http://example.org/UNKNOWN/PW/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "UBERON": "http://example.org/UNKNOWN/UBERON/", - "UniProtKB": "http://example.org/UNKNOWN/UniProtKB/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "gocam": "http://w3id.org/ontogpt/gocam/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/gocam/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "gene1": { - "@type": "@id" - }, - "gene2": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "gene": { - "@type": "@id" - }, - "molecular_activity": { - "@type": "@id" - }, - "target": { - "@type": "@id" - }, - "organism": { - "@type": "@id" - }, - "location": { - "@type": "@id" - }, - "activities": { - "@type": "@id" - }, - "cellular_processes": { - "@type": "@id" - }, - "gene_functions": { - "@type": "@id" - }, - "gene_gene_interactions": { - "@type": "@id" - }, - "gene_localizations": { - "@type": "@id" - }, - "gene_organisms": { - "@type": "@id" - }, - "genes": { - "@type": "@id" - }, - "organisms": { - "@type": "@id" - }, - "pathways": { - "@type": "@id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/gocam/jsonld/gocam.jsonld b/projects/gocam/jsonld/gocam.jsonld deleted file mode 100644 index aeb88ea1d..000000000 --- a/projects/gocam/jsonld/gocam.jsonld +++ /dev/null @@ -1,1767 +0,0 @@ -{ - "name": "gocam-template", - "description": "A template for GO-CAMs", - "title": "GO-CAM Template", - "id": "http://w3id.org/ontogpt/gocam", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "gocam", - "prefix_reference": "http://w3id.org/ontogpt/gocam/" - }, - { - "prefix_prefix": "GO", - "prefix_reference": "http://purl.obolibrary.org/obo/GO_" - }, - { - "prefix_prefix": "CL", - "prefix_reference": "http://purl.obolibrary.org/obo/CL_" - } - ], - "default_prefix": "gocam", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "GeneLocationEnum", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneLocationEnum", - "from_schema": "http://w3id.org/ontogpt/gocam", - "inherits": [ - "GOCellComponent", - "CellType" - ] - }, - { - "name": "GOCellComponentType", - "definition_uri": "http://w3id.org/ontogpt/gocam/GOCellComponentType", - "from_schema": "http://w3id.org/ontogpt/gocam", - "reachable_from": { - "source_ontology": "obo:go", - "source_nodes": [ - "GO:0005575" - ] - } - }, - { - "name": "CellType", - "definition_uri": "http://w3id.org/ontogpt/gocam/CellType", - "from_schema": "http://w3id.org/ontogpt/gocam", - "reachable_from": { - "source_ontology": "obo:cl", - "source_nodes": [ - "CL:0000000" - ] - } - }, - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "goCamAnnotations__genes", - "description": "semicolon-separated list of genes", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/genes", - "multivalued": true, - "alias": "genes", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "goCamAnnotations__organisms", - "description": "semicolon-separated list of organism taxons", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/organisms", - "multivalued": true, - "alias": "organisms", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "goCamAnnotations__gene_organisms", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of asterisk separated gene to organism relationships", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene_organisms", - "multivalued": true, - "alias": "gene_organisms", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "GeneOrganismRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "goCamAnnotations__activities", - "description": "semicolon-separated list of molecular activities", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/activities", - "multivalued": true, - "alias": "activities", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "goCamAnnotations__gene_functions", - "description": "semicolon-separated list of gene to molecular activity relationships", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene_functions", - "multivalued": true, - "alias": "gene_functions", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "GeneMolecularActivityRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "goCamAnnotations__cellular_processes", - "description": "semicolon-separated list of cellular processes", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/cellular_processes", - "multivalued": true, - "alias": "cellular_processes", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "CellularProcess", - "@type": "SlotDefinition" - }, - { - "name": "goCamAnnotations__pathways", - "description": "semicolon-separated list of pathways", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/pathways", - "multivalued": true, - "alias": "pathways", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "Pathway", - "@type": "SlotDefinition" - }, - { - "name": "goCamAnnotations__gene_gene_interactions", - "description": "semicolon-separated list of gene to gene interactions", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene_gene_interactions", - "multivalued": true, - "alias": "gene_gene_interactions", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "GeneGeneInteraction", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "goCamAnnotations__gene_localizations", - "description": "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene_localizations", - "multivalued": true, - "alias": "gene_localizations", - "owner": "GoCamAnnotations", - "domain_of": [ - "GoCamAnnotations" - ], - "range": "GeneSubcellularLocalizationRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "geneOrganismRelationship__gene", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene", - "alias": "gene", - "owner": "GeneOrganismRelationship", - "domain_of": [ - "GeneOrganismRelationship" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneOrganismRelationship__organism", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/organism", - "alias": "organism", - "owner": "GeneOrganismRelationship", - "domain_of": [ - "GeneOrganismRelationship" - ], - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship__gene", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the gene in the pair. This comes first.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene", - "alias": "gene", - "owner": "GeneMolecularActivityRelationship", - "domain_of": [ - "GeneMolecularActivityRelationship" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship__molecular_activity", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular function in the pair. This comes second. May be a GO term.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/molecular_activity", - "alias": "molecular_activity", - "owner": "GeneMolecularActivityRelationship", - "domain_of": [ - "GeneMolecularActivityRelationship" - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship2__gene", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the gene.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene", - "alias": "gene", - "owner": "GeneMolecularActivityRelationship2", - "domain_of": [ - "GeneMolecularActivityRelationship2" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship2__molecular_activity", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular activity, for example, ubiquitination. May be a GO term.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/molecular_activity", - "alias": "molecular_activity", - "owner": "GeneMolecularActivityRelationship2", - "domain_of": [ - "GeneMolecularActivityRelationship2" - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship2__target", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular entity that is the target of the molecular activity.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/target", - "alias": "target", - "owner": "GeneMolecularActivityRelationship2", - "domain_of": [ - "GeneMolecularActivityRelationship2" - ], - "range": "Molecule", - "@type": "SlotDefinition" - }, - { - "name": "geneSubcellularLocalizationRelationship__gene", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene", - "alias": "gene", - "owner": "GeneSubcellularLocalizationRelationship", - "domain_of": [ - "GeneSubcellularLocalizationRelationship" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneSubcellularLocalizationRelationship__location", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/location", - "alias": "location", - "owner": "GeneSubcellularLocalizationRelationship", - "domain_of": [ - "GeneSubcellularLocalizationRelationship" - ], - "range": "GeneLocation", - "@type": "SlotDefinition" - }, - { - "name": "geneGeneInteraction__gene1", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene1", - "alias": "gene1", - "owner": "GeneGeneInteraction", - "domain_of": [ - "GeneGeneInteraction" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneGeneInteraction__gene2", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene2", - "alias": "gene2", - "owner": "GeneGeneInteraction", - "domain_of": [ - "GeneGeneInteraction" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "GeneLocation_id", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "namedEntity__id", - "values_from": [ - "GOCellComponentType", - "CellType" - ], - "domain": "GeneLocation", - "slot_uri": "http://w3id.org/ontogpt/gocam/id", - "identifier": true, - "alias": "id", - "owner": "GeneLocation", - "domain_of": [ - "GeneLocation" - ], - "is_usage_slot": true, - "usage_slot_name": "id", - "range": "string", - "required": true, - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "GoCamAnnotations", - "definition_uri": "http://w3id.org/ontogpt/gocam/GoCamAnnotations", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slots": [ - "goCamAnnotations__genes", - "goCamAnnotations__organisms", - "goCamAnnotations__gene_organisms", - "goCamAnnotations__activities", - "goCamAnnotations__gene_functions", - "goCamAnnotations__cellular_processes", - "goCamAnnotations__pathways", - "goCamAnnotations__gene_gene_interactions", - "goCamAnnotations__gene_localizations" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "genes", - "description": "semicolon-separated list of genes", - "multivalued": true, - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "organisms", - "description": "semicolon-separated list of organism taxons", - "multivalued": true, - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "gene_organisms", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of asterisk separated gene to organism relationships", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "GeneOrganismRelationship", - "@type": "SlotDefinition" - }, - { - "name": "activities", - "description": "semicolon-separated list of molecular activities", - "multivalued": true, - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "gene_functions", - "description": "semicolon-separated list of gene to molecular activity relationships", - "multivalued": true, - "range": "GeneMolecularActivityRelationship", - "@type": "SlotDefinition" - }, - { - "name": "cellular_processes", - "description": "semicolon-separated list of cellular processes", - "multivalued": true, - "range": "CellularProcess", - "@type": "SlotDefinition" - }, - { - "name": "pathways", - "description": "semicolon-separated list of pathways", - "multivalued": true, - "range": "Pathway", - "@type": "SlotDefinition" - }, - { - "name": "gene_gene_interactions", - "description": "semicolon-separated list of gene to gene interactions", - "multivalued": true, - "range": "GeneGeneInteraction", - "@type": "SlotDefinition" - }, - { - "name": "gene_localizations", - "description": "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"", - "multivalued": true, - "range": "GeneSubcellularLocalizationRelationship", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GoCamAnnotations", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Gene", - "id_prefixes": [ - "HGNC", - "PR", - "UniProtKB" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/Gene", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, bioportal:hgnc-nr", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/Gene", - "@type": "ClassDefinition" - }, - { - "name": "Pathway", - "id_prefixes": [ - "GO", - "PW" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/Pathway", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go, sqlite:obo:pw", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/Pathway", - "@type": "ClassDefinition" - }, - { - "name": "CellularProcess", - "id_prefixes": [ - "GO" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/CellularProcess", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/CellularProcess", - "@type": "ClassDefinition" - }, - { - "name": "MolecularActivity", - "id_prefixes": [ - "GO" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/MolecularActivity", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/MolecularActivity", - "@type": "ClassDefinition" - }, - { - "name": "GeneLocation", - "id_prefixes": [ - "GO", - "CL", - "UBERON" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneLocation", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go, sqlite:obo:cl", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__label", - "GeneLocation_id" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/GeneLocation", - "@type": "ClassDefinition" - }, - { - "name": "Organism", - "id_prefixes": [ - "NCBITaxon", - "EFO" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/Organism", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, sqlite:obo:ncbitaxon", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/Organism", - "@type": "ClassDefinition" - }, - { - "name": "Molecule", - "id_prefixes": [ - "CHEBI", - "PR" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/Molecule", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, sqlite:obo:chebi", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/Molecule", - "@type": "ClassDefinition" - }, - { - "name": "GeneOrganismRelationship", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneOrganismRelationship", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneOrganismRelationship__gene", - "geneOrganismRelationship__organism" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "organism", - "range": "Organism", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneOrganismRelationship", - "@type": "ClassDefinition" - }, - { - "name": "GeneMolecularActivityRelationship", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship", - "annotations": [ - { - "tag": "prompt.example", - "value": "TODO\n\ngene: HGNC:1234\nmolecular_activity: GO:0003674", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneMolecularActivityRelationship__gene", - "geneMolecularActivityRelationship__molecular_activity" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the gene in the pair. This comes first.", - "@type": "Annotation" - } - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "molecular_activity", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular function in the pair. This comes second. May be a GO term.", - "@type": "Annotation" - } - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship", - "@type": "ClassDefinition" - }, - { - "name": "GeneMolecularActivityRelationship2", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship2", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneMolecularActivityRelationship2__gene", - "geneMolecularActivityRelationship2__molecular_activity", - "geneMolecularActivityRelationship2__target" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the gene.", - "@type": "Annotation" - } - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "molecular_activity", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular activity, for example, ubiquitination. May be a GO term.", - "@type": "Annotation" - } - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "target", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular entity that is the target of the molecular activity.", - "@type": "Annotation" - } - ], - "range": "Molecule", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship2", - "@type": "ClassDefinition" - }, - { - "name": "GeneSubcellularLocalizationRelationship", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneSubcellularLocalizationRelationship", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneSubcellularLocalizationRelationship__gene", - "geneSubcellularLocalizationRelationship__location" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "location", - "range": "GeneLocation", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneSubcellularLocalizationRelationship", - "@type": "ClassDefinition" - }, - { - "name": "GeneGeneInteraction", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneGeneInteraction", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneGeneInteraction__gene1", - "geneGeneInteraction__gene2" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene1", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "gene2", - "range": "Gene", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneGeneInteraction", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "gocam.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 4871, - "generation_date": "2023-08-07T10:53:37", - "@type": "SchemaDefinition", - "@context": [ - "projects/gocam/jsonld/gocam.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/gocam/" - } - ] -} diff --git a/projects/gocam/jsonschema/gocam.schema.json b/projects/gocam/jsonschema/gocam.schema.json deleted file mode 100644 index 205c90561..000000000 --- a/projects/gocam/jsonschema/gocam.schema.json +++ /dev/null @@ -1,499 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "CellType": { - "description": "", - "enum": [], - "title": "CellType", - "type": "string" - }, - "CellularProcess": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "CellularProcess", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "GOCellComponentType": { - "description": "", - "enum": [], - "title": "GOCellComponentType", - "type": "string" - }, - "Gene": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Gene", - "type": "object" - }, - "GeneGeneInteraction": { - "additionalProperties": false, - "description": "", - "properties": { - "gene1": { - "type": "string" - }, - "gene2": { - "type": "string" - } - }, - "title": "GeneGeneInteraction", - "type": "object" - }, - "GeneLocation": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "GeneLocation", - "type": "object" - }, - "GeneLocationEnum": { - "description": "", - "enum": [], - "title": "GeneLocationEnum", - "type": "string" - }, - "GeneMolecularActivityRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "type": "string" - }, - "molecular_activity": { - "type": "string" - } - }, - "title": "GeneMolecularActivityRelationship", - "type": "object" - }, - "GeneMolecularActivityRelationship2": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "type": "string" - }, - "molecular_activity": { - "type": "string" - }, - "target": { - "type": "string" - } - }, - "title": "GeneMolecularActivityRelationship2", - "type": "object" - }, - "GeneOrganismRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "type": "string" - }, - "organism": { - "type": "string" - } - }, - "title": "GeneOrganismRelationship", - "type": "object" - }, - "GeneSubcellularLocalizationRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "type": "string" - }, - "location": { - "type": "string" - } - }, - "title": "GeneSubcellularLocalizationRelationship", - "type": "object" - }, - "GoCamAnnotations": { - "additionalProperties": false, - "description": "", - "properties": { - "activities": { - "description": "semicolon-separated list of molecular activities", - "items": { - "type": "string" - }, - "type": "array" - }, - "cellular_processes": { - "description": "semicolon-separated list of cellular processes", - "items": { - "type": "string" - }, - "type": "array" - }, - "gene_functions": { - "description": "semicolon-separated list of gene to molecular activity relationships", - "items": { - "$ref": "#/$defs/GeneMolecularActivityRelationship" - }, - "type": "array" - }, - "gene_gene_interactions": { - "description": "semicolon-separated list of gene to gene interactions", - "items": { - "$ref": "#/$defs/GeneGeneInteraction" - }, - "type": "array" - }, - "gene_localizations": { - "description": "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"", - "items": { - "$ref": "#/$defs/GeneSubcellularLocalizationRelationship" - }, - "type": "array" - }, - "gene_organisms": { - "items": { - "$ref": "#/$defs/GeneOrganismRelationship" - }, - "type": "array" - }, - "genes": { - "description": "semicolon-separated list of genes", - "items": { - "type": "string" - }, - "type": "array" - }, - "organisms": { - "description": "semicolon-separated list of organism taxons", - "items": { - "type": "string" - }, - "type": "array" - }, - "pathways": { - "description": "semicolon-separated list of pathways", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "GoCamAnnotations", - "type": "object" - }, - "MolecularActivity": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "MolecularActivity", - "type": "object" - }, - "Molecule": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Molecule", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Organism": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Organism", - "type": "object" - }, - "Pathway": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Pathway", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/gocam", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "activities": { - "description": "semicolon-separated list of molecular activities", - "items": { - "type": "string" - }, - "type": "array" - }, - "cellular_processes": { - "description": "semicolon-separated list of cellular processes", - "items": { - "type": "string" - }, - "type": "array" - }, - "gene_functions": { - "description": "semicolon-separated list of gene to molecular activity relationships", - "items": { - "$ref": "#/$defs/GeneMolecularActivityRelationship" - }, - "type": "array" - }, - "gene_gene_interactions": { - "description": "semicolon-separated list of gene to gene interactions", - "items": { - "$ref": "#/$defs/GeneGeneInteraction" - }, - "type": "array" - }, - "gene_localizations": { - "description": "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"", - "items": { - "$ref": "#/$defs/GeneSubcellularLocalizationRelationship" - }, - "type": "array" - }, - "gene_organisms": { - "items": { - "$ref": "#/$defs/GeneOrganismRelationship" - }, - "type": "array" - }, - "genes": { - "description": "semicolon-separated list of genes", - "items": { - "type": "string" - }, - "type": "array" - }, - "organisms": { - "description": "semicolon-separated list of organism taxons", - "items": { - "type": "string" - }, - "type": "array" - }, - "pathways": { - "description": "semicolon-separated list of pathways", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "gocam-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/gocam/owl/gocam.owl.ttl b/projects/gocam/owl/gocam.owl.ttl deleted file mode 100644 index 2db2938c3..000000000 --- a/projects/gocam/owl/gocam.owl.ttl +++ /dev/null @@ -1,638 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix gocam: <http://w3id.org/ontogpt/gocam/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/gocam> a owl:Ontology ; - rdfs:label "gocam-template" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - gocam:GoCamAnnotations ; - linkml:classes "{'GoCamAnnotations': ClassDefinition(name='GoCamAnnotations', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GoCamAnnotations', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['goCamAnnotations__genes', 'goCamAnnotations__organisms', 'goCamAnnotations__gene_organisms', 'goCamAnnotations__activities', 'goCamAnnotations__gene_functions', 'goCamAnnotations__cellular_processes', 'goCamAnnotations__pathways', 'goCamAnnotations__gene_gene_interactions', 'goCamAnnotations__gene_localizations'], slot_usage={}, attributes={'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organisms': SlotDefinition(name='organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of organism taxons', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_organisms': SlotDefinition(name='gene_organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of asterisk separated gene to organism relationships', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneOrganismRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'activities': SlotDefinition(name='activities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of molecular activities', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_functions': SlotDefinition(name='gene_functions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to molecular activity relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneMolecularActivityRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'cellular_processes': SlotDefinition(name='cellular_processes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of cellular processes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CellularProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'pathways': SlotDefinition(name='pathways', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of pathways', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Pathway', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_gene_interactions': SlotDefinition(name='gene_gene_interactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to gene interactions', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneGeneInteraction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_localizations': SlotDefinition(name='gene_localizations', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneSubcellularLocalizationRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GoCamAnnotations', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC', 'PR', 'UniProtKB'], definition_uri='http://w3id.org/ontogpt/gocam/Gene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, bioportal:hgnc-nr', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Pathway': ClassDefinition(name='Pathway', id_prefixes=['GO', 'PW'], definition_uri='http://w3id.org/ontogpt/gocam/Pathway', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:pw', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:Pathway', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CellularProcess': ClassDefinition(name='CellularProcess', id_prefixes=['GO'], definition_uri='http://w3id.org/ontogpt/gocam/CellularProcess', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:CellularProcess', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'MolecularActivity': ClassDefinition(name='MolecularActivity', id_prefixes=['GO'], definition_uri='http://w3id.org/ontogpt/gocam/MolecularActivity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:MolecularActivity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneLocation': ClassDefinition(name='GeneLocation', id_prefixes=['GO', 'CL', 'UBERON'], definition_uri='http://w3id.org/ontogpt/gocam/GeneLocation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:cl', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__label', 'GeneLocation_id'], slot_usage={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='namedEntity__id', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['GOCellComponentType', 'CellType'], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='gocam:GeneLocation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Organism': ClassDefinition(name='Organism', id_prefixes=['NCBITaxon', 'EFO'], definition_uri='http://w3id.org/ontogpt/gocam/Organism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, sqlite:obo:ncbitaxon', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:Organism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Molecule': ClassDefinition(name='Molecule', id_prefixes=['CHEBI', 'PR'], definition_uri='http://w3id.org/ontogpt/gocam/Molecule', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, sqlite:obo:chebi', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:Molecule', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneOrganismRelationship': ClassDefinition(name='GeneOrganismRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneOrganismRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneOrganismRelationship__gene', 'geneOrganismRelationship__organism'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organism': SlotDefinition(name='organism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneOrganismRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneMolecularActivityRelationship': ClassDefinition(name='GeneMolecularActivityRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.example': Annotation(tag='prompt.example', value='TODO\\n\\ngene: HGNC:1234\\nmolecular_activity: GO:0003674', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneMolecularActivityRelationship__gene', 'geneMolecularActivityRelationship__molecular_activity'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the gene in the pair. This comes first.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular function in the pair. This comes second. May be a GO term.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneMolecularActivityRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneMolecularActivityRelationship2': ClassDefinition(name='GeneMolecularActivityRelationship2', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship2', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneMolecularActivityRelationship2__gene', 'geneMolecularActivityRelationship2__molecular_activity', 'geneMolecularActivityRelationship2__target'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the gene.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular activity, for example, ubiquitination. May be a GO term.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'target': SlotDefinition(name='target', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular entity that is the target of the molecular activity.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Molecule', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneMolecularActivityRelationship2', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneSubcellularLocalizationRelationship': ClassDefinition(name='GeneSubcellularLocalizationRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneSubcellularLocalizationRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneSubcellularLocalizationRelationship__gene', 'geneSubcellularLocalizationRelationship__location'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneLocation', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneSubcellularLocalizationRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneGeneInteraction': ClassDefinition(name='GeneGeneInteraction', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneGeneInteraction', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneGeneInteraction__gene1', 'geneGeneInteraction__gene2'], slot_usage={}, attributes={'gene1': SlotDefinition(name='gene1', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene2': SlotDefinition(name='gene2', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneGeneInteraction', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'GeneLocationEnum': EnumDefinition(name='GeneLocationEnum', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneLocationEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=['GOCellComponent', 'CellType'], reachable_from=None, matches=None, concepts=[]), 'GOCellComponentType': EnumDefinition(name='GOCellComponentType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GOCellComponentType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:go', source_nodes=['GO:0005575'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'CellType': EnumDefinition(name='CellType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/CellType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:cl', source_nodes=['CL:0000000'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/gocam" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -gocam:CellType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "CellType" ; - owl:unionOf [ rdf:rest () ] . - -gocam:GOCellComponentType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "GOCellComponentType" ; - owl:unionOf [ rdf:rest () ] . - -gocam:GeneLocationEnum a owl:Class, - linkml:EnumDefinition ; - rdfs:label "GeneLocationEnum" ; - owl:unionOf [ rdf:rest () ] . - -gocam:GeneMolecularActivityRelationship2 a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneMolecularActivityRelationship2" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:MolecularActivity ; - owl:onProperty gocam:molecular_activity ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Molecule ; - owl:onProperty gocam:target ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the gene.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular activity, for example, ubiquitination. May be a GO term.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'target': SlotDefinition(name='target', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular entity that is the target of the molecular activity.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Molecule', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - gocam:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -gocam:GoCamAnnotations a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GoCamAnnotations" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom gocam:Pathway ; - owl:onProperty gocam:pathways ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:GeneSubcellularLocalizationRelationship ; - owl:onProperty gocam:gene_localizations ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:GeneGeneInteraction ; - owl:onProperty gocam:gene_gene_interactions ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:Organism ; - owl:onProperty gocam:organisms ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:CellularProcess ; - owl:onProperty gocam:cellular_processes ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:GeneMolecularActivityRelationship ; - owl:onProperty gocam:gene_functions ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:Gene ; - owl:onProperty gocam:genes ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:GeneOrganismRelationship ; - owl:onProperty gocam:gene_organisms ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:MolecularActivity ; - owl:onProperty gocam:activities ] ; - linkml:attributes "{'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organisms': SlotDefinition(name='organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of organism taxons', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_organisms': SlotDefinition(name='gene_organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of asterisk separated gene to organism relationships', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneOrganismRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'activities': SlotDefinition(name='activities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of molecular activities', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_functions': SlotDefinition(name='gene_functions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to molecular activity relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneMolecularActivityRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'cellular_processes': SlotDefinition(name='cellular_processes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of cellular processes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CellularProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'pathways': SlotDefinition(name='pathways', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of pathways', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Pathway', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_gene_interactions': SlotDefinition(name='gene_gene_interactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to gene interactions', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneGeneInteraction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_localizations': SlotDefinition(name='gene_localizations', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneSubcellularLocalizationRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -gocam:activities a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "activities" ; - rdfs:range gocam:MolecularActivity ; - skos:definition "semicolon-separated list of molecular activities" . - -gocam:cellular_processes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "cellular_processes" ; - rdfs:range gocam:CellularProcess ; - skos:definition "semicolon-separated list of cellular processes" . - -gocam:gene1 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene1" ; - rdfs:range gocam:Gene . - -gocam:gene2 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene2" ; - rdfs:range gocam:Gene . - -gocam:gene_functions a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_functions" ; - rdfs:range gocam:GeneMolecularActivityRelationship ; - skos:definition "semicolon-separated list of gene to molecular activity relationships" . - -gocam:gene_gene_interactions a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_gene_interactions" ; - rdfs:range gocam:GeneGeneInteraction ; - skos:definition "semicolon-separated list of gene to gene interactions" . - -gocam:gene_localizations a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_localizations" ; - rdfs:range gocam:GeneSubcellularLocalizationRelationship ; - skos:definition "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"" . - -gocam:gene_organisms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_organisms" ; - gocam:prompt "semicolon-separated list of asterisk separated gene to organism relationships" ; - rdfs:range gocam:GeneOrganismRelationship . - -gocam:genes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "genes" ; - rdfs:range gocam:Gene ; - skos:definition "semicolon-separated list of genes" . - -gocam:id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "id" ; - rdfs:domain gocam:GeneLocation ; - rdfs:range linkml:String ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/id> ; - linkml:is_a "namedEntity__id" . - -gocam:location a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "location" ; - rdfs:range gocam:GeneLocation . - -gocam:organism a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "organism" ; - rdfs:range gocam:Organism . - -gocam:organisms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "organisms" ; - rdfs:range gocam:Organism ; - skos:definition "semicolon-separated list of organism taxons" . - -gocam:pathways a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "pathways" ; - rdfs:range gocam:Pathway ; - skos:definition "semicolon-separated list of pathways" . - -gocam:target a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "target" ; - gocam:prompt "the name of the molecular entity that is the target of the molecular activity." ; - rdfs:range gocam:Molecule . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - gocam:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:CellularProcess a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CellularProcess" ; - gocam:annotators "sqlite:obo:go" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:GeneGeneInteraction a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneGeneInteraction" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene2 ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene1': SlotDefinition(name='gene1', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene2': SlotDefinition(name='gene2', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:GeneMolecularActivityRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneMolecularActivityRelationship" ; - gocam:prompt.example """TODO - -gene: HGNC:1234 -molecular_activity: GO:0003674""" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:MolecularActivity ; - owl:onProperty gocam:molecular_activity ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the gene in the pair. This comes first.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular function in the pair. This comes second. May be a GO term.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:GeneOrganismRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneOrganismRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Organism ; - owl:onProperty gocam:organism ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organism': SlotDefinition(name='organism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:GeneSubcellularLocalizationRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneSubcellularLocalizationRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:GeneLocation ; - owl:onProperty gocam:location ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneLocation', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:Molecule a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Molecule" ; - gocam:annotators "gilda:, sqlite:obo:chebi" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:Pathway a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Pathway" ; - gocam:annotators "sqlite:obo:go, sqlite:obo:pw" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:molecular_activity a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -gocam:GeneLocation a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneLocation" ; - gocam:annotators "sqlite:obo:go, sqlite:obo:cl" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty gocam:id ; - owl:qualifiedCardinality 1 ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:MolecularActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MolecularActivity" ; - gocam:annotators "sqlite:obo:go" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:Organism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Organism" ; - gocam:annotators "gilda:, sqlite:obo:ncbitaxon" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:gene a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -gocam:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - gocam:annotators "gilda:, bioportal:hgnc-nr" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/gocam/prefixmap/gocam.yaml b/projects/gocam/prefixmap/gocam.yaml deleted file mode 100644 index e38e646ee..000000000 --- a/projects/gocam/prefixmap/gocam.yaml +++ /dev/null @@ -1,45 +0,0 @@ -{ - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "CL": "http://purl.obolibrary.org/obo/CL_", - "EFO": "http://example.org/UNKNOWN/EFO/", - "GO": "http://purl.obolibrary.org/obo/GO_", - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "NCBITaxon": "http://example.org/UNKNOWN/NCBITaxon/", - "PR": "http://example.org/UNKNOWN/PR/", - "PW": "http://example.org/UNKNOWN/PW/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "UBERON": "http://example.org/UNKNOWN/UBERON/", - "UniProtKB": "http://example.org/UNKNOWN/UniProtKB/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "gocam": "http://w3id.org/ontogpt/gocam/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/gocam/protobuf/gocam.proto b/projects/gocam/protobuf/gocam.proto deleted file mode 100644 index 135e40a64..000000000 --- a/projects/gocam/protobuf/gocam.proto +++ /dev/null @@ -1,108 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message CellularProcess - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -message GeneGeneInteraction - { - gene gene1 = 0 - gene gene2 = 0 - } -message GeneLocation - { - string label = 0 - string id = 0 - } -message GeneMolecularActivityRelationship - { - gene gene = 0 - molecularActivity molecularActivity = 0 - } -message GeneMolecularActivityRelationship2 - { - gene gene = 0 - molecularActivity molecularActivity = 0 - molecule target = 0 - } -message GeneOrganismRelationship - { - gene gene = 0 - organism organism = 0 - } -message GeneSubcellularLocalizationRelationship - { - gene gene = 0 - geneLocation location = 0 - } -message GoCamAnnotations - { - repeated gene genes = 0 - repeated organism organisms = 0 - repeated geneOrganismRelationship geneOrganisms = 0 - repeated molecularActivity activities = 0 - repeated geneMolecularActivityRelationship geneFunctions = 0 - repeated cellularProcess cellularProcesses = 0 - repeated pathway pathways = 0 - repeated geneGeneInteraction geneGeneInteractions = 0 - repeated geneSubcellularLocalizationRelationship geneLocalizations = 0 - } -message MolecularActivity - { - string id = 0 - string label = 0 - } -message Molecule - { - string id = 0 - string label = 0 - } -message Organism - { - string id = 0 - string label = 0 - } -message Pathway - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/gocam/shacl/gocam.shacl.ttl b/projects/gocam/shacl/gocam.shacl.ttl deleted file mode 100644 index ffecaeba0..000000000 --- a/projects/gocam/shacl/gocam.shacl.ttl +++ /dev/null @@ -1,391 +0,0 @@ -@prefix gocam: <http://w3id.org/ontogpt/gocam/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -gocam:GeneMolecularActivityRelationship2 a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:Molecule ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path gocam:target ], - [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene ], - [ sh:class gocam:MolecularActivity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:molecular_activity ] ; - sh:targetClass gocam:GeneMolecularActivityRelationship2 . - -gocam:GoCamAnnotations a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:CellularProcess ; - sh:description "semicolon-separated list of cellular processes" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path gocam:cellular_processes ], - [ sh:class gocam:GeneSubcellularLocalizationRelationship ; - sh:description "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"" ; - sh:nodeKind sh:BlankNode ; - sh:order 8 ; - sh:path gocam:gene_localizations ], - [ sh:class gocam:MolecularActivity ; - sh:description "semicolon-separated list of molecular activities" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path gocam:activities ], - [ sh:class gocam:GeneOrganismRelationship ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path gocam:gene_organisms ], - [ sh:class gocam:GeneGeneInteraction ; - sh:description "semicolon-separated list of gene to gene interactions" ; - sh:nodeKind sh:BlankNode ; - sh:order 7 ; - sh:path gocam:gene_gene_interactions ], - [ sh:class gocam:GeneMolecularActivityRelationship ; - sh:description "semicolon-separated list of gene to molecular activity relationships" ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path gocam:gene_functions ], - [ sh:class gocam:Gene ; - sh:description "semicolon-separated list of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:genes ], - [ sh:class gocam:Organism ; - sh:description "semicolon-separated list of organism taxons" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:organisms ], - [ sh:class gocam:Pathway ; - sh:description "semicolon-separated list of pathways" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path gocam:pathways ] ; - sh:targetClass gocam:GoCamAnnotations . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -gocam:CellularProcess a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:CellularProcess . - -gocam:GeneGeneInteraction a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene1 ], - [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:gene2 ] ; - sh:targetClass gocam:GeneGeneInteraction . - -gocam:GeneLocation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:GeneLocation . - -gocam:GeneMolecularActivityRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene ], - [ sh:class gocam:MolecularActivity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:molecular_activity ] ; - sh:targetClass gocam:GeneMolecularActivityRelationship . - -gocam:GeneOrganismRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene ], - [ sh:class gocam:Organism ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:organism ] ; - sh:targetClass gocam:GeneOrganismRelationship . - -gocam:GeneSubcellularLocalizationRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:GeneLocation ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:location ], - [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene ] ; - sh:targetClass gocam:GeneSubcellularLocalizationRelationship . - -gocam:Molecule a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass gocam:Molecule . - -gocam:Pathway a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass gocam:Pathway . - -gocam:Organism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:Organism . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -gocam:MolecularActivity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:MolecularActivity . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - -gocam:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:Gene . - diff --git a/projects/gocam/shex/gocam.shex b/projects/gocam/shex/gocam.shex deleted file mode 100644 index fb81046aa..000000000 --- a/projects/gocam/shex/gocam.shex +++ /dev/null @@ -1,260 +0,0 @@ -BASE <http://w3id.org/ontogpt/gocam/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<CellularProcess> CLOSED { - ( $<CellularProcess_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <CellularProcess> ] - ) -} - -core:CompoundExpression ( - @<GeneGeneInteraction> OR @<GeneMolecularActivityRelationship> OR @<GeneMolecularActivityRelationship2> OR - @<GeneOrganismRelationship> OR @<GeneSubcellularLocalizationRelationship> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<Gene> CLOSED { - ( $<Gene_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Gene> ] - ) -} - -<GeneGeneInteraction> CLOSED { - ( $<GeneGeneInteraction_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene1> @<Gene> ? ; - <gene2> @<Gene> ? - ) ; - rdf:type [ <GeneGeneInteraction> ] ? - ) -} - -<GeneLocation> CLOSED { - ( $<GeneLocation_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <GeneLocation> ] - ) -} - -<GeneMolecularActivityRelationship> CLOSED { - ( $<GeneMolecularActivityRelationship_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <molecular_activity> @<MolecularActivity> ? - ) ; - rdf:type [ <GeneMolecularActivityRelationship> ] ? - ) -} - -<GeneMolecularActivityRelationship2> CLOSED { - ( $<GeneMolecularActivityRelationship2_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <molecular_activity> @<MolecularActivity> ? ; - <target> @<Molecule> ? - ) ; - rdf:type [ <GeneMolecularActivityRelationship2> ] ? - ) -} - -<GeneOrganismRelationship> CLOSED { - ( $<GeneOrganismRelationship_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <organism> @<Organism> ? - ) ; - rdf:type [ <GeneOrganismRelationship> ] ? - ) -} - -<GeneSubcellularLocalizationRelationship> CLOSED { - ( $<GeneSubcellularLocalizationRelationship_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <location> @<GeneLocation> ? - ) ; - rdf:type [ <GeneSubcellularLocalizationRelationship> ] ? - ) -} - -<GoCamAnnotations> CLOSED { - ( $<GoCamAnnotations_tes> ( <genes> @<Gene> * ; - <organisms> @<Organism> * ; - <gene_organisms> @<GeneOrganismRelationship> * ; - <activities> @<MolecularActivity> * ; - <gene_functions> @<GeneMolecularActivityRelationship> * ; - <cellular_processes> @<CellularProcess> * ; - <pathways> @<Pathway> * ; - <gene_gene_interactions> @<GeneGeneInteraction> * ; - <gene_localizations> @<GeneSubcellularLocalizationRelationship> * - ) ; - rdf:type [ <GoCamAnnotations> ] ? - ) -} - -<MolecularActivity> CLOSED { - ( $<MolecularActivity_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <MolecularActivity> ] - ) -} - -<Molecule> CLOSED { - ( $<Molecule_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Molecule> ] - ) -} - -core:NamedEntity ( - @<CellularProcess> OR @<Gene> OR @<GeneLocation> OR @<MolecularActivity> OR @<Molecule> OR @<Organism> OR @<Pathway> OR - @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<Organism> CLOSED { - ( $<Organism_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Organism> ] - ) -} - -<Pathway> CLOSED { - ( $<Pathway_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Pathway> ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/gocam/sqlschema/gocam.sql b/projects/gocam/sqlschema/gocam.sql deleted file mode 100644 index d1a86a14d..000000000 --- a/projects/gocam/sqlschema/gocam.sql +++ /dev/null @@ -1,137 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "CellularProcess" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "GeneLocation" ( - label TEXT, - id TEXT NOT NULL, - PRIMARY KEY (id) -); - -CREATE TABLE "GoCamAnnotations" ( - genes TEXT, - organisms TEXT, - gene_organisms TEXT, - activities TEXT, - gene_functions TEXT, - cellular_processes TEXT, - pathways TEXT, - gene_gene_interactions TEXT, - gene_localizations TEXT, - PRIMARY KEY (genes, organisms, gene_organisms, activities, gene_functions, cellular_processes, pathways, gene_gene_interactions, gene_localizations) -); - -CREATE TABLE "MolecularActivity" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Molecule" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Organism" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Pathway" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "GeneGeneInteraction" ( - gene1 TEXT, - gene2 TEXT, - PRIMARY KEY (gene1, gene2), - FOREIGN KEY(gene1) REFERENCES "Gene" (id), - FOREIGN KEY(gene2) REFERENCES "Gene" (id) -); - -CREATE TABLE "GeneMolecularActivityRelationship" ( - gene TEXT, - molecular_activity TEXT, - PRIMARY KEY (gene, molecular_activity), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(molecular_activity) REFERENCES "MolecularActivity" (id) -); - -CREATE TABLE "GeneMolecularActivityRelationship2" ( - gene TEXT, - molecular_activity TEXT, - target TEXT, - PRIMARY KEY (gene, molecular_activity, target), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(molecular_activity) REFERENCES "MolecularActivity" (id), - FOREIGN KEY(target) REFERENCES "Molecule" (id) -); - -CREATE TABLE "GeneOrganismRelationship" ( - gene TEXT, - organism TEXT, - PRIMARY KEY (gene, organism), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(organism) REFERENCES "Organism" (id) -); - -CREATE TABLE "GeneSubcellularLocalizationRelationship" ( - gene TEXT, - location TEXT, - PRIMARY KEY (gene, location), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(location) REFERENCES "GeneLocation" (id) -); diff --git a/projects/halo/docs/AnnotatorResult.md b/projects/halo/docs/AnnotatorResult.md deleted file mode 100644 index 4f189092b..000000000 --- a/projects/halo/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [oc:AnnotatorResult](http://w3id.org/ontogpt/ontology-class-templateAnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/halo/docs/Any.md b/projects/halo/docs/Any.md deleted file mode 100644 index 75c20f2f8..000000000 --- a/projects/halo/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [oc:Any](http://w3id.org/ontogpt/ontology-class-templateAny) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/halo/docs/Category.md b/projects/halo/docs/Category.md deleted file mode 100644 index 0b363a659..000000000 --- a/projects/halo/docs/Category.md +++ /dev/null @@ -1,54 +0,0 @@ - -# Class: Category - - - - -URI: [oc:Category](http://w3id.org/ontogpt/ontology-class-templateCategory) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyElement],[OntologyElement]-%20categories%200..*>[Category|name(i):string;context(i):string%20%3F;description(i):string%20%3F;synonyms(i):string%20*;equivalent_to(i):string%20%3F],[OntologyElement]^-[Category])](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyElement],[OntologyElement]-%20categories%200..*>[Category|name(i):string;context(i):string%20%3F;description(i):string%20%3F;synonyms(i):string%20*;equivalent_to(i):string%20%3F],[OntologyElement]^-[Category]) - -## Parents - - * is_a: [OntologyElement](OntologyElement.md) - -## Referenced by Class - - * **None** *[➞categories](ontologyElement__categories.md)* <sub>0..\*</sub> **[Category](Category.md)** - -## Attributes - - -### Inherited from OntologyElement: - - * [➞name](ontologyElement__name.md) <sub>1..1</sub> - * Description: the name of the entity - * Range: [String](types/String.md) - * [➞context](ontologyElement__context.md) <sub>0..1</sub> - * Description: the ontology to which this belongs (single-valued) - * Range: [String](types/String.md) - * [➞description](ontologyElement__description.md) <sub>0..1</sub> - * Description: a textual description of the entity (single-valued) - * Range: [String](types/String.md) - * [➞synonyms](ontologyElement__synonyms.md) <sub>0..\*</sub> - * Description: a list of alternative names of the entity - * Range: [String](types/String.md) - * [➞categories](ontologyElement__categories.md) <sub>0..\*</sub> - * Description: a list of the categories to which this entity belongs - * Range: [Category](Category.md) - * [➞subclass_of](ontologyElement__subclass_of.md) <sub>0..\*</sub> - * Description: a list of parent class (superclasses) of this entity - * Range: [OntologyElement](OntologyElement.md) - * [➞part_of](ontologyElement__part_of.md) <sub>0..\*</sub> - * Description: a list of things this element is part of - * Range: [OntologyElement](OntologyElement.md) - * [➞subtypes](ontologyElement__subtypes.md) <sub>0..\*</sub> - * Description: a list of child classes (subclasses) of this entity - * Range: [OntologyElement](OntologyElement.md) - * [➞parts](ontologyElement__parts.md) <sub>0..\*</sub> - * Description: a list of names of things this element has as parts (components) - * Range: [OntologyElement](OntologyElement.md) - * [➞equivalent_to](ontologyElement__equivalent_to.md) <sub>0..1</sub> - * Description: an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class - * Range: [String](types/String.md) diff --git a/projects/halo/docs/CompoundExpression.md b/projects/halo/docs/CompoundExpression.md deleted file mode 100644 index 35fe2b15a..000000000 --- a/projects/halo/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [oc:CompoundExpression](http://w3id.org/ontogpt/ontology-class-templateCompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/halo/docs/ExtractionResult.md b/projects/halo/docs/ExtractionResult.md deleted file mode 100644 index fe7d19bb9..000000000 --- a/projects/halo/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [oc:ExtractionResult](http://w3id.org/ontogpt/ontology-class-templateExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/halo/docs/NamedEntity.md b/projects/halo/docs/NamedEntity.md deleted file mode 100644 index 12879e464..000000000 --- a/projects/halo/docs/NamedEntity.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [oc:NamedEntity](http://w3id.org/ontogpt/ontology-class-templateNamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[Triple]) - -## Children - - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/halo/docs/NullDataOptions.md b/projects/halo/docs/NullDataOptions.md deleted file mode 100644 index 4b9a6758e..000000000 --- a/projects/halo/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [oc:NullDataOptions](http://w3id.org/ontogpt/ontology-class-templateNullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/halo/docs/Ontology.md b/projects/halo/docs/Ontology.md deleted file mode 100644 index f210fae5d..000000000 --- a/projects/halo/docs/Ontology.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Class: Ontology - - - - -URI: [oc:Ontology](http://w3id.org/ontogpt/ontology-class-templateOntology) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyElement],[OntologyElement]<elements%200..*-++[Ontology])](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyElement],[OntologyElement]<elements%200..*-++[Ontology]) - -## Attributes - - -### Own - - * [➞elements](ontology__elements.md) <sub>0..\*</sub> - * Range: [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/OntologyElement.md b/projects/halo/docs/OntologyElement.md deleted file mode 100644 index 98acc2bf4..000000000 --- a/projects/halo/docs/OntologyElement.md +++ /dev/null @@ -1,60 +0,0 @@ - -# Class: OntologyElement - - - - -URI: [oc:OntologyElement](http://w3id.org/ontogpt/ontology-class-templateOntologyElement) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyElement]<parts%200..*-%20[OntologyElement|name:string;context:string%20%3F;description:string%20%3F;synonyms:string%20*;equivalent_to:string%20%3F],[OntologyElement]<subtypes%200..*-%20[OntologyElement],[OntologyElement]<part_of%200..*-%20[OntologyElement],[OntologyElement]<subclass_of%200..*-%20[OntologyElement],[Category]<categories%200..*-%20[OntologyElement],[Ontology]++-%20elements%200..*>[OntologyElement],[OntologyElement]^-[Category],[Ontology],[Category])](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyElement]<parts%200..*-%20[OntologyElement|name:string;context:string%20%3F;description:string%20%3F;synonyms:string%20*;equivalent_to:string%20%3F],[OntologyElement]<subtypes%200..*-%20[OntologyElement],[OntologyElement]<part_of%200..*-%20[OntologyElement],[OntologyElement]<subclass_of%200..*-%20[OntologyElement],[Category]<categories%200..*-%20[OntologyElement],[Ontology]++-%20elements%200..*>[OntologyElement],[OntologyElement]^-[Category],[Ontology],[Category]) - -## Children - - * [Category](Category.md) - -## Referenced by Class - - * **None** *[➞part_of](ontologyElement__part_of.md)* <sub>0..\*</sub> **[OntologyElement](OntologyElement.md)** - * **None** *[➞parts](ontologyElement__parts.md)* <sub>0..\*</sub> **[OntologyElement](OntologyElement.md)** - * **None** *[➞subclass_of](ontologyElement__subclass_of.md)* <sub>0..\*</sub> **[OntologyElement](OntologyElement.md)** - * **None** *[➞subtypes](ontologyElement__subtypes.md)* <sub>0..\*</sub> **[OntologyElement](OntologyElement.md)** - * **None** *[➞elements](ontology__elements.md)* <sub>0..\*</sub> **[OntologyElement](OntologyElement.md)** - * **[OntologyElement](OntologyElement.md)** *[part_of](part_of.md)* <sub>0..\*</sub> **[OntologyElement](OntologyElement.md)** - * **[OntologyElement](OntologyElement.md)** *[subclass_of](subclass_of.md)* <sub>0..\*</sub> **[OntologyElement](OntologyElement.md)** - -## Attributes - - -### Own - - * [➞name](ontologyElement__name.md) <sub>1..1</sub> - * Description: the name of the entity - * Range: [String](types/String.md) - * [➞context](ontologyElement__context.md) <sub>0..1</sub> - * Description: the ontology to which this belongs (single-valued) - * Range: [String](types/String.md) - * [➞description](ontologyElement__description.md) <sub>0..1</sub> - * Description: a textual description of the entity (single-valued) - * Range: [String](types/String.md) - * [➞synonyms](ontologyElement__synonyms.md) <sub>0..\*</sub> - * Description: a list of alternative names of the entity - * Range: [String](types/String.md) - * [➞categories](ontologyElement__categories.md) <sub>0..\*</sub> - * Description: a list of the categories to which this entity belongs - * Range: [Category](Category.md) - * [➞subclass_of](ontologyElement__subclass_of.md) <sub>0..\*</sub> - * Description: a list of parent class (superclasses) of this entity - * Range: [OntologyElement](OntologyElement.md) - * [➞part_of](ontologyElement__part_of.md) <sub>0..\*</sub> - * Description: a list of things this element is part of - * Range: [OntologyElement](OntologyElement.md) - * [➞subtypes](ontologyElement__subtypes.md) <sub>0..\*</sub> - * Description: a list of child classes (subclasses) of this entity - * Range: [OntologyElement](OntologyElement.md) - * [➞parts](ontologyElement__parts.md) <sub>0..\*</sub> - * Description: a list of names of things this element has as parts (components) - * Range: [OntologyElement](OntologyElement.md) - * [➞equivalent_to](ontologyElement__equivalent_to.md) <sub>0..1</sub> - * Description: an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class - * Range: [String](types/String.md) diff --git a/projects/halo/docs/Publication.md b/projects/halo/docs/Publication.md deleted file mode 100644 index a55c2f8cc..000000000 --- a/projects/halo/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [oc:Publication](http://w3id.org/ontogpt/ontology-class-templatePublication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/halo/docs/RelationshipType.md b/projects/halo/docs/RelationshipType.md deleted file mode 100644 index 4adecdef0..000000000 --- a/projects/halo/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [oc:RelationshipType](http://w3id.org/ontogpt/ontology-class-templateRelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/halo/docs/TextWithTriples.md b/projects/halo/docs/TextWithTriples.md deleted file mode 100644 index e94121934..000000000 --- a/projects/halo/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [oc:TextWithTriples](http://w3id.org/ontogpt/ontology-class-templateTextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/halo/docs/Triple.md b/projects/halo/docs/Triple.md deleted file mode 100644 index 5a0ca3d43..000000000 --- a/projects/halo/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [oc:Triple](http://w3id.org/ontogpt/ontology-class-templateTriple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/halo/docs/annotatorResult__object_id.md b/projects/halo/docs/annotatorResult__object_id.md deleted file mode 100644 index be14e5b97..000000000 --- a/projects/halo/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [oc:annotatorResult__object_id](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/halo/docs/annotatorResult__object_text.md b/projects/halo/docs/annotatorResult__object_text.md deleted file mode 100644 index fbf16b458..000000000 --- a/projects/halo/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [oc:annotatorResult__object_text](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/halo/docs/annotatorResult__subject_text.md b/projects/halo/docs/annotatorResult__subject_text.md deleted file mode 100644 index 1525bf843..000000000 --- a/projects/halo/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [oc:annotatorResult__subject_text](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/halo/docs/extractionResult__extracted_object.md b/projects/halo/docs/extractionResult__extracted_object.md deleted file mode 100644 index b1bc7ddff..000000000 --- a/projects/halo/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [oc:extractionResult__extracted_object](http://w3id.org/ontogpt/ontology-class-templateextractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/halo/docs/extractionResult__input_id.md b/projects/halo/docs/extractionResult__input_id.md deleted file mode 100644 index 06eab71c1..000000000 --- a/projects/halo/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [oc:extractionResult__input_id](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/halo/docs/extractionResult__input_text.md b/projects/halo/docs/extractionResult__input_text.md deleted file mode 100644 index 1dc6a7221..000000000 --- a/projects/halo/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [oc:extractionResult__input_text](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/halo/docs/extractionResult__input_title.md b/projects/halo/docs/extractionResult__input_title.md deleted file mode 100644 index 2d7893d36..000000000 --- a/projects/halo/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [oc:extractionResult__input_title](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/halo/docs/extractionResult__named_entities.md b/projects/halo/docs/extractionResult__named_entities.md deleted file mode 100644 index 37772a93c..000000000 --- a/projects/halo/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [oc:extractionResult__named_entities](http://w3id.org/ontogpt/ontology-class-templateextractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/halo/docs/extractionResult__prompt.md b/projects/halo/docs/extractionResult__prompt.md deleted file mode 100644 index 8ba0ddcab..000000000 --- a/projects/halo/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [oc:extractionResult__prompt](http://w3id.org/ontogpt/ontology-class-templateextractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/halo/docs/extractionResult__raw_completion_output.md b/projects/halo/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index ec9df2512..000000000 --- a/projects/halo/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [oc:extractionResult__raw_completion_output](http://w3id.org/ontogpt/ontology-class-templateextractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/halo/docs/halo.md b/projects/halo/docs/halo.md deleted file mode 100644 index 03a30c543..000000000 --- a/projects/halo/docs/halo.md +++ /dev/null @@ -1,119 +0,0 @@ - -# ontology-class - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for Ontology Classes - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Ontology](Ontology.md) - * [OntologyElement](OntologyElement.md) - * [Category](Category.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞categories](ontologyElement__categories.md) - a list of the categories to which this entity belongs - * [➞context](ontologyElement__context.md) - the ontology to which this belongs (single-valued) - * [➞description](ontologyElement__description.md) - a textual description of the entity (single-valued) - * [➞equivalent_to](ontologyElement__equivalent_to.md) - an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class - * [➞name](ontologyElement__name.md) - the name of the entity - * [➞part_of](ontologyElement__part_of.md) - a list of things this element is part of - * [➞parts](ontologyElement__parts.md) - a list of names of things this element has as parts (components) - * [➞subclass_of](ontologyElement__subclass_of.md) - a list of parent class (superclasses) of this entity - * [➞subtypes](ontologyElement__subtypes.md) - a list of child classes (subclasses) of this entity - * [➞synonyms](ontologyElement__synonyms.md) - a list of alternative names of the entity - * [➞elements](ontology__elements.md) - * [part_of](part_of.md) - a list of things this element is part of - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [subclass_of](subclass_of.md) - a list of parent class (superclasses) of this entity - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/halo/docs/namedEntity__id.md b/projects/halo/docs/namedEntity__id.md deleted file mode 100644 index 0764cce7f..000000000 --- a/projects/halo/docs/namedEntity__id.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [oc:namedEntity__id](http://w3id.org/ontogpt/ontology-class-templatenamedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/halo/docs/namedEntity__label.md b/projects/halo/docs/namedEntity__label.md deleted file mode 100644 index 0ce06a4ef..000000000 --- a/projects/halo/docs/namedEntity__label.md +++ /dev/null @@ -1,31 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [oc:namedEntity__label](http://w3id.org/ontogpt/ontology-class-templatenamedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/halo/docs/ontologyElement__categories.md b/projects/halo/docs/ontologyElement__categories.md deleted file mode 100644 index d5d3eef1a..000000000 --- a/projects/halo/docs/ontologyElement__categories.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: categories - - -a list of the categories to which this entity belongs - -URI: [oc:ontologyElement__categories](http://w3id.org/ontogpt/ontology-class-templateontologyElement__categories) - - -## Domain and Range - -None → <sub>0..\*</sub> [Category](Category.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/ontologyElement__context.md b/projects/halo/docs/ontologyElement__context.md deleted file mode 100644 index 519b959dd..000000000 --- a/projects/halo/docs/ontologyElement__context.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: context - - -the ontology to which this belongs (single-valued) - -URI: [oc:ontologyElement__context](http://w3id.org/ontogpt/ontology-class-templateontologyElement__context) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/ontologyElement__description.md b/projects/halo/docs/ontologyElement__description.md deleted file mode 100644 index 897c5f635..000000000 --- a/projects/halo/docs/ontologyElement__description.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: description - - -a textual description of the entity (single-valued) - -URI: [oc:ontologyElement__description](http://w3id.org/ontogpt/ontology-class-templateontologyElement__description) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/ontologyElement__equivalent_to.md b/projects/halo/docs/ontologyElement__equivalent_to.md deleted file mode 100644 index 5e9443d52..000000000 --- a/projects/halo/docs/ontologyElement__equivalent_to.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: equivalent_to - - -an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class - -URI: [oc:ontologyElement__equivalent_to](http://w3id.org/ontogpt/ontology-class-templateontologyElement__equivalent_to) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/ontologyElement__name.md b/projects/halo/docs/ontologyElement__name.md deleted file mode 100644 index de297854e..000000000 --- a/projects/halo/docs/ontologyElement__name.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: name - - -the name of the entity - -URI: [oc:ontologyElement__name](http://w3id.org/ontogpt/ontology-class-templateontologyElement__name) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/ontologyElement__part_of.md b/projects/halo/docs/ontologyElement__part_of.md deleted file mode 100644 index 0456bb123..000000000 --- a/projects/halo/docs/ontologyElement__part_of.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: part_of - - -a list of things this element is part of - -URI: [oc:ontologyElement__part_of](http://w3id.org/ontogpt/ontology-class-templateontologyElement__part_of) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyElement](OntologyElement.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | BFO:0000050 | - diff --git a/projects/halo/docs/ontologyElement__parts.md b/projects/halo/docs/ontologyElement__parts.md deleted file mode 100644 index 32c6f3f15..000000000 --- a/projects/halo/docs/ontologyElement__parts.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: parts - - -a list of names of things this element has as parts (components) - -URI: [oc:ontologyElement__parts](http://w3id.org/ontogpt/ontology-class-templateontologyElement__parts) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyElement](OntologyElement.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/ontologyElement__subclass_of.md b/projects/halo/docs/ontologyElement__subclass_of.md deleted file mode 100644 index 50bf9936d..000000000 --- a/projects/halo/docs/ontologyElement__subclass_of.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: subclass_of - - -a list of parent class (superclasses) of this entity - -URI: [oc:ontologyElement__subclass_of](http://w3id.org/ontogpt/ontology-class-templateontologyElement__subclass_of) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyElement](OntologyElement.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | rdfs:subClassOf | - diff --git a/projects/halo/docs/ontologyElement__subtypes.md b/projects/halo/docs/ontologyElement__subtypes.md deleted file mode 100644 index 71f378eb9..000000000 --- a/projects/halo/docs/ontologyElement__subtypes.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subtypes - - -a list of child classes (subclasses) of this entity - -URI: [oc:ontologyElement__subtypes](http://w3id.org/ontogpt/ontology-class-templateontologyElement__subtypes) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyElement](OntologyElement.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/ontologyElement__synonyms.md b/projects/halo/docs/ontologyElement__synonyms.md deleted file mode 100644 index dae57a11b..000000000 --- a/projects/halo/docs/ontologyElement__synonyms.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: synonyms - - -a list of alternative names of the entity - -URI: [oc:ontologyElement__synonyms](http://w3id.org/ontogpt/ontology-class-templateontologyElement__synonyms) - - -## Domain and Range - -None → <sub>0..\*</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Category](Category.md) - * [OntologyElement](OntologyElement.md) diff --git a/projects/halo/docs/ontology__elements.md b/projects/halo/docs/ontology__elements.md deleted file mode 100644 index 57d0fb5da..000000000 --- a/projects/halo/docs/ontology__elements.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: elements - - - - -URI: [oc:ontology__elements](http://w3id.org/ontogpt/ontology-class-templateontology__elements) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyElement](OntologyElement.md) - -## Parents - - -## Children - - -## Used by - - * [Ontology](Ontology.md) diff --git a/projects/halo/docs/part_of.md b/projects/halo/docs/part_of.md deleted file mode 100644 index 58621e4f3..000000000 --- a/projects/halo/docs/part_of.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Slot: part_of - - -a list of things this element is part of - -URI: [oc:part_of](http://w3id.org/ontogpt/ontology-class-templatepart_of) - - -## Domain and Range - -[OntologyElement](OntologyElement.md) → <sub>0..\*</sub> [OntologyElement](OntologyElement.md) - -## Parents - - -## Children - - -## Used by - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | BFO:0000050 | - diff --git a/projects/halo/docs/publication__abstract.md b/projects/halo/docs/publication__abstract.md deleted file mode 100644 index 7e1c7ff37..000000000 --- a/projects/halo/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [oc:publication__abstract](http://w3id.org/ontogpt/ontology-class-templatepublication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/halo/docs/publication__combined_text.md b/projects/halo/docs/publication__combined_text.md deleted file mode 100644 index de03f19fd..000000000 --- a/projects/halo/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [oc:publication__combined_text](http://w3id.org/ontogpt/ontology-class-templatepublication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/halo/docs/publication__full_text.md b/projects/halo/docs/publication__full_text.md deleted file mode 100644 index ae02a60d4..000000000 --- a/projects/halo/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [oc:publication__full_text](http://w3id.org/ontogpt/ontology-class-templatepublication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/halo/docs/publication__id.md b/projects/halo/docs/publication__id.md deleted file mode 100644 index 3fbcffacd..000000000 --- a/projects/halo/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [oc:publication__id](http://w3id.org/ontogpt/ontology-class-templatepublication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/halo/docs/publication__title.md b/projects/halo/docs/publication__title.md deleted file mode 100644 index 5f9f7ed69..000000000 --- a/projects/halo/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [oc:publication__title](http://w3id.org/ontogpt/ontology-class-templatepublication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/halo/docs/subclass_of.md b/projects/halo/docs/subclass_of.md deleted file mode 100644 index 76fe3918b..000000000 --- a/projects/halo/docs/subclass_of.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Slot: subclass_of - - -a list of parent class (superclasses) of this entity - -URI: [oc:subclass_of](http://w3id.org/ontogpt/ontology-class-templatesubclass_of) - - -## Domain and Range - -[OntologyElement](OntologyElement.md) → <sub>0..\*</sub> [OntologyElement](OntologyElement.md) - -## Parents - - -## Children - - -## Used by - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | rdfs:subClassOf | - diff --git a/projects/halo/docs/textWithTriples__publication.md b/projects/halo/docs/textWithTriples__publication.md deleted file mode 100644 index 27b0af18d..000000000 --- a/projects/halo/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [oc:textWithTriples__publication](http://w3id.org/ontogpt/ontology-class-templatetextWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/halo/docs/textWithTriples__triples.md b/projects/halo/docs/textWithTriples__triples.md deleted file mode 100644 index d3a729b64..000000000 --- a/projects/halo/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [oc:textWithTriples__triples](http://w3id.org/ontogpt/ontology-class-templatetextWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/halo/docs/triple__object.md b/projects/halo/docs/triple__object.md deleted file mode 100644 index 19c663552..000000000 --- a/projects/halo/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [oc:triple__object](http://w3id.org/ontogpt/ontology-class-templatetriple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/halo/docs/triple__object_qualifier.md b/projects/halo/docs/triple__object_qualifier.md deleted file mode 100644 index bead5d4a5..000000000 --- a/projects/halo/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [oc:triple__object_qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/halo/docs/triple__predicate.md b/projects/halo/docs/triple__predicate.md deleted file mode 100644 index 425642196..000000000 --- a/projects/halo/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [oc:triple__predicate](http://w3id.org/ontogpt/ontology-class-templatetriple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/halo/docs/triple__qualifier.md b/projects/halo/docs/triple__qualifier.md deleted file mode 100644 index 9277dabfe..000000000 --- a/projects/halo/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [oc:triple__qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/halo/docs/triple__subject.md b/projects/halo/docs/triple__subject.md deleted file mode 100644 index 89487785e..000000000 --- a/projects/halo/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [oc:triple__subject](http://w3id.org/ontogpt/ontology-class-templatetriple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/halo/docs/triple__subject_qualifier.md b/projects/halo/docs/triple__subject_qualifier.md deleted file mode 100644 index e63c6bbd8..000000000 --- a/projects/halo/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [oc:triple__subject_qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/halo/docs/types/Boolean.md b/projects/halo/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/halo/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/halo/docs/types/Curie.md b/projects/halo/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/halo/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/halo/docs/types/Date.md b/projects/halo/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/halo/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/halo/docs/types/DateOrDatetime.md b/projects/halo/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/halo/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/halo/docs/types/Datetime.md b/projects/halo/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/halo/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/halo/docs/types/Decimal.md b/projects/halo/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/halo/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/halo/docs/types/Double.md b/projects/halo/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/halo/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/halo/docs/types/Float.md b/projects/halo/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/halo/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/halo/docs/types/Integer.md b/projects/halo/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/halo/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/halo/docs/types/Jsonpath.md b/projects/halo/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/halo/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/halo/docs/types/Jsonpointer.md b/projects/halo/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/halo/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/halo/docs/types/Ncname.md b/projects/halo/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/halo/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/halo/docs/types/Nodeidentifier.md b/projects/halo/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/halo/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/halo/docs/types/Objectidentifier.md b/projects/halo/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/halo/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/halo/docs/types/Sparqlpath.md b/projects/halo/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/halo/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/halo/docs/types/String.md b/projects/halo/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/halo/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/halo/docs/types/Time.md b/projects/halo/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/halo/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/halo/docs/types/Uri.md b/projects/halo/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/halo/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/halo/docs/types/Uriorcurie.md b/projects/halo/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/halo/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/halo/excel/halo.xlsx b/projects/halo/excel/halo.xlsx deleted file mode 100644 index 8bc324a24cbb1fb3dc6758b8574a16f44fd9dff7..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 8855 zcmeHtWl$V#*Cy^ZxH}=i-Q6X)4{pKT-Q6_=Cs=R@E&&D)Zovtf;K2zN*h!xH-n?P+ zRPFxUs-3Ftp01g5%{|vS_t93Chlat1fPg@N0BOQ&NdZA9!Qi_(@PPq7%p6RWogExq zn2jABnLO=m72*|;dsr|e9_98{?KMuwS;=P$*FXBmaC0S^iMxm0`>KHwmIXeu#J1rK 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zISl234%H$Gh+I?!H`+#{=;>-+=KNf*lS?nT0G%AU5@KlAmX>e#8I}jW`&z~4d(9H$ zp*Jz>0%v_tdhz_RMP;PkxWOXjcahSR^52EXIA)mgc~ZuXez+Qc8i$r_zc@bqPC$0a ze8C#uH|Rz!WKVhOL==@EOD*&b{EjRtAtK=7bYo?|rsmzNu~_x1ZoDIYqX+Pa6%q;? z`rn7bU?cqX3Ir?Qe;*M)m3}&+{YMr8A`r6nzoq|YVEa`3=?wF?_&E6I|1!~h3h=at z{U3m!pT+|Q_-jY|DazBv>~EAnaC-9>lwWPy|8o=-aFqHB%CFwwQ<SGIsNZX$1m{_Q zLHX5?dW!P2|MDBf2JNpXzq&C`QJ!`HexophpC9<kT7LBdo}xUhV}GO6fT#L@LHSkH zK1F$2l>J6|4xWDh1?5+X_7vr5{qP&57rZ6@g7T}Hc#85g`TY+H<V)OND8EzTr=m}D zm*1j8;D+OWWin3%pXLI;1?vd@v-1DR44w)<4Ku%mQ;2>E|4Yz$iu2Sn|HgSo3<2>M ZKdmee3yy3*AKw5#*u#L`IqA>4{{;{`5Y_+y diff --git a/projects/halo/graphql/halo.graphql b/projects/halo/graphql/halo.graphql deleted file mode 100644 index 16f95365e..000000000 --- a/projects/halo/graphql/halo.graphql +++ /dev/null @@ -1,96 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type Category - { - name: String! - context: String - description: String - synonyms: [String] - categories: [Category] - subclassOf: [OntologyElement] - partOf: [OntologyElement] - subtypes: [OntologyElement] - parts: [OntologyElement] - equivalentTo: String - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -interface NamedEntity - { - id: String! - label: String - } - -type Ontology - { - elements: [OntologyElement] - } - -type OntologyElement - { - name: String! - context: String - description: String - synonyms: [String] - categories: [Category] - subclassOf: [OntologyElement] - partOf: [OntologyElement] - subtypes: [OntologyElement] - parts: [OntologyElement] - equivalentTo: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/halo/halo.py b/projects/halo/halo.py deleted file mode 100644 index 42d6d1376..000000000 --- a/projects/halo/halo.py +++ /dev/null @@ -1,509 +0,0 @@ -# Auto generated from halo.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:54:01 -# Schema: ontology-class -# -# id: https://w3id.org/ontogpt/halo -# description: A template for Ontology Classes -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -BFO = CurieNamespace('BFO', 'http://purl.obolibrary.org/obo/BFO_') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -OC = CurieNamespace('oc', 'http://w3id.org/ontogpt/ontology-class-template') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = OC - - -# Types - -# Class references -class OntologyElementName(extended_str): - pass - - -class CategoryName(OntologyElementName): - pass - - -class NamedEntityId(extended_str): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class Ontology(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.Ontology - class_class_curie: ClassVar[str] = "oc:Ontology" - class_name: ClassVar[str] = "Ontology" - class_model_uri: ClassVar[URIRef] = OC.Ontology - - elements: Optional[Union[Dict[Union[str, OntologyElementName], Union[dict, "OntologyElement"]], List[Union[dict, "OntologyElement"]]]] = empty_dict() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - self._normalize_inlined_as_list(slot_name="elements", slot_type=OntologyElement, key_name="name", keyed=True) - - super().__post_init__(**kwargs) - - -@dataclass -class OntologyElement(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.OntologyElement - class_class_curie: ClassVar[str] = "oc:OntologyElement" - class_name: ClassVar[str] = "OntologyElement" - class_model_uri: ClassVar[URIRef] = OC.OntologyElement - - name: Union[str, OntologyElementName] = None - context: Optional[str] = None - description: Optional[str] = None - synonyms: Optional[Union[str, List[str]]] = empty_list() - categories: Optional[Union[Union[str, CategoryName], List[Union[str, CategoryName]]]] = empty_list() - subclass_of: Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]] = empty_list() - part_of: Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]] = empty_list() - subtypes: Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]] = empty_list() - parts: Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]] = empty_list() - equivalent_to: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.name): - self.MissingRequiredField("name") - if not isinstance(self.name, OntologyElementName): - self.name = OntologyElementName(self.name) - - if self.context is not None and not isinstance(self.context, str): - self.context = str(self.context) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.synonyms, list): - self.synonyms = [self.synonyms] if self.synonyms is not None else [] - self.synonyms = [v if isinstance(v, str) else str(v) for v in self.synonyms] - - if not isinstance(self.categories, list): - self.categories = [self.categories] if self.categories is not None else [] - self.categories = [v if isinstance(v, CategoryName) else CategoryName(v) for v in self.categories] - - if not isinstance(self.subclass_of, list): - self.subclass_of = [self.subclass_of] if self.subclass_of is not None else [] - self.subclass_of = [v if isinstance(v, OntologyElementName) else OntologyElementName(v) for v in self.subclass_of] - - if not isinstance(self.part_of, list): - self.part_of = [self.part_of] if self.part_of is not None else [] - self.part_of = [v if isinstance(v, OntologyElementName) else OntologyElementName(v) for v in self.part_of] - - if not isinstance(self.subtypes, list): - self.subtypes = [self.subtypes] if self.subtypes is not None else [] - self.subtypes = [v if isinstance(v, OntologyElementName) else OntologyElementName(v) for v in self.subtypes] - - if not isinstance(self.parts, list): - self.parts = [self.parts] if self.parts is not None else [] - self.parts = [v if isinstance(v, OntologyElementName) else OntologyElementName(v) for v in self.parts] - - if self.equivalent_to is not None and not isinstance(self.equivalent_to, str): - self.equivalent_to = str(self.equivalent_to) - - super().__post_init__(**kwargs) - - -@dataclass -class Category(OntologyElement): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.Category - class_class_curie: ClassVar[str] = "oc:Category" - class_name: ClassVar[str] = "Category" - class_model_uri: ClassVar[URIRef] = OC.Category - - name: Union[str, CategoryName] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.name): - self.MissingRequiredField("name") - if not isinstance(self.name, CategoryName): - self.name = CategoryName(self.name) - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = OC.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = OC.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = OC.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = OC.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = OC.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = OC.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = OC.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = OC.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.subclass_of = Slot(uri=RDFS.subClassOf, name="subclass_of", curie=RDFS.curie('subClassOf'), - model_uri=OC.subclass_of, domain=OntologyElement, range=Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]]) - -slots.part_of = Slot(uri=BFO['0000050'], name="part_of", curie=BFO.curie('0000050'), - model_uri=OC.part_of, domain=OntologyElement, range=Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]]) - -slots.ontology__elements = Slot(uri=OC.elements, name="ontology__elements", curie=OC.curie('elements'), - model_uri=OC.ontology__elements, domain=None, range=Optional[Union[Dict[Union[str, OntologyElementName], Union[dict, OntologyElement]], List[Union[dict, OntologyElement]]]]) - -slots.ontologyElement__name = Slot(uri=OC.name, name="ontologyElement__name", curie=OC.curie('name'), - model_uri=OC.ontologyElement__name, domain=None, range=URIRef) - -slots.ontologyElement__context = Slot(uri=OC.context, name="ontologyElement__context", curie=OC.curie('context'), - model_uri=OC.ontologyElement__context, domain=None, range=Optional[str]) - -slots.ontologyElement__description = Slot(uri=OC.description, name="ontologyElement__description", curie=OC.curie('description'), - model_uri=OC.ontologyElement__description, domain=None, range=Optional[str]) - -slots.ontologyElement__synonyms = Slot(uri=OC.synonyms, name="ontologyElement__synonyms", curie=OC.curie('synonyms'), - model_uri=OC.ontologyElement__synonyms, domain=None, range=Optional[Union[str, List[str]]]) - -slots.ontologyElement__categories = Slot(uri=OC.categories, name="ontologyElement__categories", curie=OC.curie('categories'), - model_uri=OC.ontologyElement__categories, domain=None, range=Optional[Union[Union[str, CategoryName], List[Union[str, CategoryName]]]]) - -slots.ontologyElement__subclass_of = Slot(uri=RDFS.subClassOf, name="ontologyElement__subclass_of", curie=RDFS.curie('subClassOf'), - model_uri=OC.ontologyElement__subclass_of, domain=None, range=Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]]) - -slots.ontologyElement__part_of = Slot(uri=BFO['0000050'], name="ontologyElement__part_of", curie=BFO.curie('0000050'), - model_uri=OC.ontologyElement__part_of, domain=None, range=Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]]) - -slots.ontologyElement__subtypes = Slot(uri=OC.subtypes, name="ontologyElement__subtypes", curie=OC.curie('subtypes'), - model_uri=OC.ontologyElement__subtypes, domain=None, range=Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]]) - -slots.ontologyElement__parts = Slot(uri=OC.parts, name="ontologyElement__parts", curie=OC.curie('parts'), - model_uri=OC.ontologyElement__parts, domain=None, range=Optional[Union[Union[str, OntologyElementName], List[Union[str, OntologyElementName]]]]) - -slots.ontologyElement__equivalent_to = Slot(uri=OC.equivalent_to, name="ontologyElement__equivalent_to", curie=OC.curie('equivalent_to'), - model_uri=OC.ontologyElement__equivalent_to, domain=None, range=Optional[str]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=OC.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=OC.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=OC.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=OC.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=OC.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=OC.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=OC.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=OC.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=OC.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=OC.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=OC.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=OC.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=OC.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=OC.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=OC.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=OC.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=OC.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=OC.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=OC.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=OC.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=OC.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=OC.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=OC.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=OC.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=OC.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/halo/jsonld/halo.context.jsonld b/projects/halo/jsonld/halo.context.jsonld deleted file mode 100644 index a9d057eb0..000000000 --- a/projects/halo/jsonld/halo.context.jsonld +++ /dev/null @@ -1,155 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:53:52", - "source": "halo.yaml" - }, - "@context": { - "BFO": { - "@id": "http://purl.obolibrary.org/obo/BFO_", - "@prefix": true - }, - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "oc": { - "@id": "http://w3id.org/ontogpt/ontology-class-template", - "@prefix": true - }, - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/ontology-class-template", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "elements": { - "@type": "@id" - }, - "categories": { - "@type": "@id" - }, - "name": "@id", - "part_of": { - "@type": "@id", - "@id": "BFO:0000050" - }, - "parts": { - "@type": "@id" - }, - "subclass_of": { - "@type": "@id", - "@id": "rdfs:subClassOf" - }, - "subtypes": { - "@type": "@id" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/halo/jsonld/halo.jsonld b/projects/halo/jsonld/halo.jsonld deleted file mode 100644 index 6409ea842..000000000 --- a/projects/halo/jsonld/halo.jsonld +++ /dev/null @@ -1,1297 +0,0 @@ -{ - "name": "ontology-class", - "description": "A template for Ontology Classes", - "title": "Ontology Class Template", - "id": "https://w3id.org/ontogpt/halo", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "oc", - "prefix_reference": "http://w3id.org/ontogpt/ontology-class-template" - }, - { - "prefix_prefix": "BFO", - "prefix_reference": "http://purl.obolibrary.org/obo/BFO_" - } - ], - "default_prefix": "oc", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "subclass_of", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templatesubclass_of", - "description": "a list of parent class (superclasses) of this entity", - "from_schema": "https://w3id.org/ontogpt/halo", - "mappings": [ - "http://example.org/UNKNOWN/rdfs/subClassOf" - ], - "domain": "OntologyElement", - "slot_uri": "http://example.org/UNKNOWN/rdfs/subClassOf", - "multivalued": true, - "inverse": "ontologyElement__subtypes", - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "part_of", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templatepart_of", - "description": "a list of things this element is part of", - "from_schema": "https://w3id.org/ontogpt/halo", - "mappings": [ - "http://purl.obolibrary.org/obo/BFO_0000050" - ], - "domain": "OntologyElement", - "slot_uri": "http://purl.obolibrary.org/obo/BFO_0000050", - "multivalued": true, - "inverse": "ontologyElement__parts", - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "ontology__elements", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templateelements", - "multivalued": true, - "alias": "elements", - "owner": "Ontology", - "domain_of": [ - "Ontology" - ], - "range": "OntologyElement", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__name", - "description": "the name of the entity", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatename", - "identifier": true, - "alias": "name", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__context", - "description": "the ontology to which this belongs (single-valued)", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatecontext", - "alias": "context", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__description", - "description": "a textual description of the entity (single-valued)", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatedescription", - "alias": "description", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__synonyms", - "description": "a list of alternative names of the entity", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatesynonyms", - "multivalued": true, - "alias": "synonyms", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__categories", - "description": "a list of the categories to which this entity belongs", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatecategories", - "multivalued": true, - "alias": "categories", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "range": "Category", - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__subclass_of", - "description": "a list of parent class (superclasses) of this entity", - "from_schema": "https://w3id.org/ontogpt/halo", - "mappings": [ - "http://example.org/UNKNOWN/rdfs/subClassOf" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/subClassOf", - "multivalued": true, - "alias": "subclass_of", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__part_of", - "description": "a list of things this element is part of", - "from_schema": "https://w3id.org/ontogpt/halo", - "mappings": [ - "http://purl.obolibrary.org/obo/BFO_0000050" - ], - "slot_uri": "http://purl.obolibrary.org/obo/BFO_0000050", - "multivalued": true, - "alias": "part_of", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__subtypes", - "description": "a list of child classes (subclasses) of this entity", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatesubtypes", - "multivalued": true, - "alias": "subtypes", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "inverse": "subclass_of", - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__parts", - "description": "a list of names of things this element has as parts (components)", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templateparts", - "multivalued": true, - "alias": "parts", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "inverse": "part_of", - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "ontologyElement__equivalent_to", - "description": "an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class", - "from_schema": "https://w3id.org/ontogpt/halo", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templateequivalent_to", - "alias": "equivalent_to", - "owner": "OntologyElement", - "domain_of": [ - "OntologyElement" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Ontology", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateOntology", - "from_schema": "https://w3id.org/ontogpt/halo", - "slots": [ - "ontology__elements" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "elements", - "multivalued": true, - "range": "OntologyElement", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateOntology", - "@type": "ClassDefinition" - }, - { - "name": "OntologyElement", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyElement", - "from_schema": "https://w3id.org/ontogpt/halo", - "slots": [ - "ontologyElement__name", - "ontologyElement__context", - "ontologyElement__description", - "ontologyElement__synonyms", - "ontologyElement__categories", - "ontologyElement__subclass_of", - "ontologyElement__part_of", - "ontologyElement__subtypes", - "ontologyElement__parts", - "ontologyElement__equivalent_to" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "name", - "description": "the name of the entity", - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "context", - "description": "the ontology to which this belongs (single-valued)", - "@type": "SlotDefinition" - }, - { - "name": "description", - "description": "a textual description of the entity (single-valued)", - "@type": "SlotDefinition" - }, - { - "name": "synonyms", - "description": "a list of alternative names of the entity", - "multivalued": true, - "@type": "SlotDefinition" - }, - { - "name": "categories", - "description": "a list of the categories to which this entity belongs", - "multivalued": true, - "range": "Category", - "@type": "SlotDefinition" - }, - { - "name": "subclass_of", - "description": "a list of parent class (superclasses) of this entity", - "slot_uri": "rdfs:subClassOf", - "multivalued": true, - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "part_of", - "description": "a list of things this element is part of", - "slot_uri": "BFO:0000050", - "multivalued": true, - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "subtypes", - "description": "a list of child classes (subclasses) of this entity", - "multivalued": true, - "inverse": "subclass_of", - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "parts", - "description": "a list of names of things this element has as parts (components)", - "multivalued": true, - "inverse": "part_of", - "range": "OntologyElement", - "@type": "SlotDefinition" - }, - { - "name": "equivalent_to", - "description": "an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyElement", - "@type": "ClassDefinition" - }, - { - "name": "Category", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateCategory", - "from_schema": "https://w3id.org/ontogpt/halo", - "is_a": "OntologyElement", - "slots": [ - "ontologyElement__name", - "ontologyElement__context", - "ontologyElement__description", - "ontologyElement__synonyms", - "ontologyElement__categories", - "ontologyElement__subclass_of", - "ontologyElement__part_of", - "ontologyElement__subtypes", - "ontologyElement__parts", - "ontologyElement__equivalent_to" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateCategory", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "halo.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 2367, - "generation_date": "2023-08-07T10:53:53", - "@type": "SchemaDefinition", - "@context": [ - "projects/halo/jsonld/halo.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/ontology-class-template" - } - ] -} diff --git a/projects/halo/jsonschema/halo.schema.json b/projects/halo/jsonschema/halo.schema.json deleted file mode 100644 index 15aa2278e..000000000 --- a/projects/halo/jsonschema/halo.schema.json +++ /dev/null @@ -1,293 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "Category": { - "additionalProperties": false, - "description": "", - "properties": { - "categories": { - "description": "a list of the categories to which this entity belongs", - "items": { - "type": "string" - }, - "type": "array" - }, - "context": { - "description": "the ontology to which this belongs (single-valued)", - "type": "string" - }, - "description": { - "description": "a textual description of the entity (single-valued)", - "type": "string" - }, - "equivalent_to": { - "description": "an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class", - "type": "string" - }, - "name": { - "description": "the name of the entity", - "type": "string" - }, - "part_of": { - "description": "a list of things this element is part of", - "items": { - "type": "string" - }, - "type": "array" - }, - "parts": { - "description": "a list of names of things this element has as parts (components)", - "items": { - "type": "string" - }, - "type": "array" - }, - "subclass_of": { - "description": "a list of parent class (superclasses) of this entity", - "items": { - "type": "string" - }, - "type": "array" - }, - "subtypes": { - "description": "a list of child classes (subclasses) of this entity", - "items": { - "type": "string" - }, - "type": "array" - }, - "synonyms": { - "description": "a list of alternative names of the entity", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "name" - ], - "title": "Category", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Ontology": { - "additionalProperties": false, - "description": "", - "properties": { - "elements": { - "items": { - "$ref": "#/$defs/OntologyElement" - }, - "type": "array" - } - }, - "title": "Ontology", - "type": "object" - }, - "OntologyElement": { - "additionalProperties": false, - "description": "", - "properties": { - "categories": { - "description": "a list of the categories to which this entity belongs", - "items": { - "type": "string" - }, - "type": "array" - }, - "context": { - "description": "the ontology to which this belongs (single-valued)", - "type": "string" - }, - "description": { - "description": "a textual description of the entity (single-valued)", - "type": "string" - }, - "equivalent_to": { - "description": "an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class", - "type": "string" - }, - "name": { - "description": "the name of the entity", - "type": "string" - }, - "part_of": { - "description": "a list of things this element is part of", - "items": { - "type": "string" - }, - "type": "array" - }, - "parts": { - "description": "a list of names of things this element has as parts (components)", - "items": { - "type": "string" - }, - "type": "array" - }, - "subclass_of": { - "description": "a list of parent class (superclasses) of this entity", - "items": { - "type": "string" - }, - "type": "array" - }, - "subtypes": { - "description": "a list of child classes (subclasses) of this entity", - "items": { - "type": "string" - }, - "type": "array" - }, - "synonyms": { - "description": "a list of alternative names of the entity", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "name" - ], - "title": "OntologyElement", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "https://w3id.org/ontogpt/halo", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "ontology-class", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/halo/owl/halo.owl.ttl b/projects/halo/owl/halo.owl.ttl deleted file mode 100644 index 1ce5232f5..000000000 --- a/projects/halo/owl/halo.owl.ttl +++ /dev/null @@ -1,471 +0,0 @@ -@prefix BFO: <http://purl.obolibrary.org/obo/BFO_> . -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix oc: <http://w3id.org/ontogpt/ontology-class-template> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<https://w3id.org/ontogpt/halo> a owl:Ontology ; - rdfs:label "ontology-class" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - oc:Ontology, - oc:OntologyElement ; - linkml:classes "{'Ontology': ClassDefinition(name='Ontology', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateOntology', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/halo', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['ontology__elements'], slot_usage={}, attributes={'elements': SlotDefinition(name='elements', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='oc:Ontology', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'OntologyElement': ClassDefinition(name='OntologyElement', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateOntologyElement', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/halo', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['ontologyElement__name', 'ontologyElement__context', 'ontologyElement__description', 'ontologyElement__synonyms', 'ontologyElement__categories', 'ontologyElement__subclass_of', 'ontologyElement__part_of', 'ontologyElement__subtypes', 'ontologyElement__parts', 'ontologyElement__equivalent_to'], slot_usage={}, attributes={'name': SlotDefinition(name='name', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'context': SlotDefinition(name='context', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the ontology to which this belongs (single-valued)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the entity (single-valued)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of alternative names of the entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'categories': SlotDefinition(name='categories', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of the categories to which this entity belongs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Category', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of parent class (superclasses) of this entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:subClassOf', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'part_of': SlotDefinition(name='part_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of things this element is part of', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='BFO:0000050', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subtypes': SlotDefinition(name='subtypes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of child classes (subclasses) of this entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse='subclass_of', is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'parts': SlotDefinition(name='parts', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of names of things this element has as parts (components)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse='part_of', is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'equivalent_to': SlotDefinition(name='equivalent_to', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='oc:OntologyElement', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Category': ClassDefinition(name='Category', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateCategory', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/halo', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='OntologyElement', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['ontologyElement__name', 'ontologyElement__context', 'ontologyElement__description', 'ontologyElement__synonyms', 'ontologyElement__categories', 'ontologyElement__subclass_of', 'ontologyElement__part_of', 'ontologyElement__subtypes', 'ontologyElement__parts', 'ontologyElement__equivalent_to'], slot_usage={}, attributes={}, class_uri='oc:Category', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/halo" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - oc:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -oc:Ontology a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Ontology" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyElement ; - owl:onProperty oc:elements ] ; - linkml:attributes "{'elements': SlotDefinition(name='elements', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -oc:categories a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "categories" ; - rdfs:range oc:Category ; - skos:definition "a list of the categories to which this entity belongs" . - -oc:context a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "context" ; - rdfs:range linkml:String ; - skos:definition "the ontology to which this belongs (single-valued)" . - -oc:description a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "description" ; - rdfs:range linkml:String ; - skos:definition "a textual description of the entity (single-valued)" . - -oc:elements a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "elements" ; - rdfs:range oc:OntologyElement . - -oc:equivalent_to a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "equivalent_to" ; - rdfs:range linkml:String ; - skos:definition "an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class" . - -oc:name a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "name" ; - rdfs:range linkml:String ; - skos:definition "the name of the entity" . - -oc:parts a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "parts" ; - rdfs:range oc:OntologyElement ; - owl:inverseOf BFO:0000050 ; - skos:definition "a list of names of things this element has as parts (components)" . - -oc:subtypes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subtypes" ; - rdfs:range oc:OntologyElement ; - owl:inverseOf <http://example.org/UNKNOWN/rdfs/subClassOf> ; - skos:definition "a list of child classes (subclasses) of this entity" . - -oc:synonyms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "synonyms" ; - rdfs:range linkml:String ; - skos:definition "a list of alternative names of the entity" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - oc:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://example.org/UNKNOWN/rdfs/subClassOf> a owl:ObjectProperty, - linkml:SlotDefinition . - -BFO:0000050 a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -oc:Category a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Category" ; - rdfs:subClassOf oc:OntologyElement ; - linkml:attributes "{}" ; - linkml:is_a "OntologyElement" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -oc:OntologyElement a owl:Class, - linkml:ClassDefinition ; - rdfs:label "OntologyElement" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty oc:synonyms ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyElement ; - owl:onProperty oc:parts ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyElement ; - owl:onProperty oc:subtypes ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:context ], - [ a owl:Restriction ; - owl:allValuesFrom oc:Category ; - owl:onProperty oc:categories ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:equivalent_to ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:description ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyElement ; - owl:onProperty BFO:0000050 ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty oc:name ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyElement ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/subClassOf> ] ; - linkml:attributes "{'name': SlotDefinition(name='name', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'context': SlotDefinition(name='context', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the ontology to which this belongs (single-valued)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the entity (single-valued)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of alternative names of the entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'categories': SlotDefinition(name='categories', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of the categories to which this entity belongs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Category', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of parent class (superclasses) of this entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:subClassOf', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'part_of': SlotDefinition(name='part_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of things this element is part of', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='BFO:0000050', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subtypes': SlotDefinition(name='subtypes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of child classes (subclasses) of this entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse='subclass_of', is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'parts': SlotDefinition(name='parts', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a list of names of things this element has as parts (components)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse='part_of', is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyElement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'equivalent_to': SlotDefinition(name='equivalent_to', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/halo/prefixmap/halo.yaml b/projects/halo/prefixmap/halo.yaml deleted file mode 100644 index 9067c91e2..000000000 --- a/projects/halo/prefixmap/halo.yaml +++ /dev/null @@ -1,36 +0,0 @@ -{ - "BFO": "http://purl.obolibrary.org/obo/BFO_", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "oc": "http://w3id.org/ontogpt/ontology-class-template", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/halo/protobuf/halo.proto b/projects/halo/protobuf/halo.proto deleted file mode 100644 index 51c92e48c..000000000 --- a/projects/halo/protobuf/halo.proto +++ /dev/null @@ -1,65 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message Category - { - string name = 0 - string context = 0 - string description = 0 - repeated string synonyms = 0 - repeated category categories = 0 - repeated ontologyElement subclassOf = 0 - repeated ontologyElement partOf = 0 - repeated ontologyElement subtypes = 0 - repeated ontologyElement parts = 0 - string equivalentTo = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Ontology - { - repeated ontologyElement elements = 0 - } -message OntologyElement - { - string name = 0 - string context = 0 - string description = 0 - repeated string synonyms = 0 - repeated category categories = 0 - repeated ontologyElement subclassOf = 0 - repeated ontologyElement partOf = 0 - repeated ontologyElement subtypes = 0 - repeated ontologyElement parts = 0 - string equivalentTo = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/halo/shacl/halo.shacl.ttl b/projects/halo/shacl/halo.shacl.ttl deleted file mode 100644 index e72f9090d..000000000 --- a/projects/halo/shacl/halo.shacl.ttl +++ /dev/null @@ -1,273 +0,0 @@ -@prefix BFO: <http://purl.obolibrary.org/obo/BFO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix oc: <http://w3id.org/ontogpt/ontology-class-template> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ], - [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -oc:Ontology a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class oc:OntologyElement ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path oc:elements ] ; - sh:targetClass oc:Ontology . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -oc:Category a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path oc:equivalent_to ], - [ sh:description "the name of the entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path oc:name ], - [ sh:class oc:Category ; - sh:description "a list of the categories to which this entity belongs" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path oc:categories ], - [ sh:class oc:OntologyElement ; - sh:description "a list of names of things this element has as parts (components)" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path oc:parts ], - [ sh:description "a textual description of the entity (single-valued)" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path oc:description ], - [ sh:description "a list of alternative names of the entity" ; - sh:order 3 ; - sh:path oc:synonyms ], - [ sh:class oc:OntologyElement ; - sh:description "a list of child classes (subclasses) of this entity" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path oc:subtypes ], - [ sh:class oc:OntologyElement ; - sh:description "a list of things this element is part of" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path BFO:0000050 ], - [ sh:class oc:OntologyElement ; - sh:description "a list of parent class (superclasses) of this entity" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <rdfs:subClassOf> ], - [ sh:description "the ontology to which this belongs (single-valued)" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path oc:context ] ; - sh:targetClass oc:Category . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - -oc:OntologyElement a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class oc:OntologyElement ; - sh:description "a list of child classes (subclasses) of this entity" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path oc:subtypes ], - [ sh:class oc:OntologyElement ; - sh:description "a list of things this element is part of" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path BFO:0000050 ], - [ sh:class oc:OntologyElement ; - sh:description "a list of parent class (superclasses) of this entity" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <rdfs:subClassOf> ], - [ sh:description "an OWL class expression with the necessary and sufficient conditions for this entity to be an instance of this class" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path oc:equivalent_to ], - [ sh:description "a textual description of the entity (single-valued)" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path oc:description ], - [ sh:description "the ontology to which this belongs (single-valued)" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path oc:context ], - [ sh:class oc:OntologyElement ; - sh:description "a list of names of things this element has as parts (components)" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path oc:parts ], - [ sh:class oc:Category ; - sh:description "a list of the categories to which this entity belongs" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path oc:categories ], - [ sh:description "a list of alternative names of the entity" ; - sh:order 3 ; - sh:path oc:synonyms ], - [ sh:description "the name of the entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path oc:name ] ; - sh:targetClass oc:OntologyElement . - diff --git a/projects/halo/shex/halo.shex b/projects/halo/shex/halo.shex deleted file mode 100644 index cce79a67b..000000000 --- a/projects/halo/shex/halo.shex +++ /dev/null @@ -1,169 +0,0 @@ -BASE <http://w3id.org/ontogpt/ontology-class-template/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateCategory> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateCategory_tes> ( - &<http://w3id.org/ontogpt/ontology-class-templateOntologyElement_tes> ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateOntologyElement> ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateCategory> ] - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -core:NamedEntity ( - { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) - } OR @core:RelationshipType -) - -<http://w3id.org/ontogpt/ontology-class-templateOntology> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateOntology_tes> <http://w3id.org/ontogpt/ontology-class-templateelements> - @<http://w3id.org/ontogpt/ontology-class-templateOntologyElement> * ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateOntology> ] ? - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateOntologyElement> ( - CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateOntologyElement_tes> ( - <http://w3id.org/ontogpt/ontology-class-templatecontext> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatedescription> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatesynonyms> @linkml:String * ; - <http://w3id.org/ontogpt/ontology-class-templatecategories> @<http://w3id.org/ontogpt/ontology-class-templateCategory> - * ; - rdfs1:subClassOf @<http://w3id.org/ontogpt/ontology-class-templateOntologyElement> * ; - <http://purl.obolibrary.org/obo/BFO_0000050> @<http://w3id.org/ontogpt/ontology-class-templateOntologyElement> * ; - <http://w3id.org/ontogpt/ontology-class-templatesubtypes> - @<http://w3id.org/ontogpt/ontology-class-templateOntologyElement> * ; - <http://w3id.org/ontogpt/ontology-class-templateparts> - @<http://w3id.org/ontogpt/ontology-class-templateOntologyElement> * ; - <http://w3id.org/ontogpt/ontology-class-templateequivalent_to> @linkml:String ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateOntologyElement> ] - ) - } OR @<http://w3id.org/ontogpt/ontology-class-templateCategory> -) - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/halo/sqlschema/halo.sql b/projects/halo/sqlschema/halo.sql deleted file mode 100644 index 97cfaad80..000000000 --- a/projects/halo/sqlschema/halo.sql +++ /dev/null @@ -1,85 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Category" ( - name TEXT NOT NULL, - context TEXT, - description TEXT, - categories TEXT, - subclass_of TEXT, - part_of TEXT, - subtypes TEXT, - parts TEXT, - equivalent_to TEXT, - PRIMARY KEY (name) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Ontology" ( - elements TEXT, - PRIMARY KEY (elements) -); - -CREATE TABLE "OntologyElement" ( - name TEXT NOT NULL, - context TEXT, - description TEXT, - categories TEXT, - subclass_of TEXT, - part_of TEXT, - subtypes TEXT, - parts TEXT, - equivalent_to TEXT, - PRIMARY KEY (name) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Category_synonyms" ( - backref_id TEXT, - synonyms TEXT, - PRIMARY KEY (backref_id, synonyms), - FOREIGN KEY(backref_id) REFERENCES "Category" (name) -); - -CREATE TABLE "OntologyElement_synonyms" ( - backref_id TEXT, - synonyms TEXT, - PRIMARY KEY (backref_id, synonyms), - FOREIGN KEY(backref_id) REFERENCES "OntologyElement" (name) -); diff --git a/projects/ibd/docs/AnnotatorResult.md b/projects/ibd/docs/AnnotatorResult.md deleted file mode 100644 index b21f75a37..000000000 --- a/projects/ibd/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [gocam:AnnotatorResult](http://w3id.org/ontogpt/gocam/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/Any.md b/projects/ibd/docs/Any.md deleted file mode 100644 index 294c64451..000000000 --- a/projects/ibd/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [gocam:Any](http://w3id.org/ontogpt/gocam/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/ibd/docs/CellType.md b/projects/ibd/docs/CellType.md deleted file mode 100644 index cce37c2b0..000000000 --- a/projects/ibd/docs/CellType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: CellType - - - - -URI: [gocam:CellType](http://w3id.org/ontogpt/gocam/CellType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/ibd/docs/CellularProcess.md b/projects/ibd/docs/CellularProcess.md deleted file mode 100644 index a97d8ea79..000000000 --- a/projects/ibd/docs/CellularProcess.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: CellularProcess - - - - -URI: [gocam:CellularProcess](http://w3id.org/ontogpt/gocam/CellularProcess) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[IBDAnnotations]-%20cellular_processes%200..*>[CellularProcess|id(i):string;label(i):string%20%3F],[NamedEntity]^-[CellularProcess],[IBDAnnotations])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[IBDAnnotations]-%20cellular_processes%200..*>[CellularProcess|id(i):string;label(i):string%20%3F],[NamedEntity]^-[CellularProcess],[IBDAnnotations]) - -## Identifier prefixes - - * GO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞cellular_processes](iBDAnnotations__cellular_processes.md)* <sub>0..\*</sub> **[CellularProcess](CellularProcess.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/CompoundExpression.md b/projects/ibd/docs/CompoundExpression.md deleted file mode 100644 index 2c710a723..000000000 --- a/projects/ibd/docs/CompoundExpression.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [gocam:CompoundExpression](http://w3id.org/ontogpt/gocam/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship],[GeneGeneInteraction],[CompoundExpression]^-[Triple],[CompoundExpression]^-[GeneSubcellularLocalizationRelationship],[CompoundExpression]^-[GeneOrganismRelationship],[CompoundExpression]^-[GeneMolecularActivityRelationship2],[CompoundExpression]^-[GeneMolecularActivityRelationship],[CompoundExpression]^-[GeneGeneInteraction])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship],[GeneGeneInteraction],[CompoundExpression]^-[Triple],[CompoundExpression]^-[GeneSubcellularLocalizationRelationship],[CompoundExpression]^-[GeneOrganismRelationship],[CompoundExpression]^-[GeneMolecularActivityRelationship2],[CompoundExpression]^-[GeneMolecularActivityRelationship],[CompoundExpression]^-[GeneGeneInteraction]) - -## Children - - * [GeneGeneInteraction](GeneGeneInteraction.md) - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) - * [GeneOrganismRelationship](GeneOrganismRelationship.md) - * [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/ibd/docs/ExtractionResult.md b/projects/ibd/docs/ExtractionResult.md deleted file mode 100644 index 5fd1b0627..000000000 --- a/projects/ibd/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [gocam:ExtractionResult](http://w3id.org/ontogpt/gocam/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/ibd/docs/GOCellComponentType.md b/projects/ibd/docs/GOCellComponentType.md deleted file mode 100644 index e2e6fcda9..000000000 --- a/projects/ibd/docs/GOCellComponentType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: GOCellComponentType - - - - -URI: [gocam:GOCellComponentType](http://w3id.org/ontogpt/gocam/GOCellComponentType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/ibd/docs/Gene.md b/projects/ibd/docs/Gene.md deleted file mode 100644 index 582d0b4b8..000000000 --- a/projects/ibd/docs/Gene.md +++ /dev/null @@ -1,42 +0,0 @@ - -# Class: Gene - - - - -URI: [gocam:Gene](http://w3id.org/ontogpt/gocam/Gene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneGeneInteraction]-%20gene1%200..1>[Gene|id(i):string;label(i):string%20%3F],[GeneGeneInteraction]-%20gene2%200..1>[Gene],[GeneMolecularActivityRelationship2]-%20gene%200..1>[Gene],[GeneMolecularActivityRelationship]-%20gene%200..1>[Gene],[GeneOrganismRelationship]-%20gene%200..1>[Gene],[GeneSubcellularLocalizationRelationship]-%20gene%200..1>[Gene],[IBDAnnotations]-%20genes%200..*>[Gene],[NamedEntity]^-[Gene],[IBDAnnotations],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship],[GeneGeneInteraction])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneGeneInteraction]-%20gene1%200..1>[Gene|id(i):string;label(i):string%20%3F],[GeneGeneInteraction]-%20gene2%200..1>[Gene],[GeneMolecularActivityRelationship2]-%20gene%200..1>[Gene],[GeneMolecularActivityRelationship]-%20gene%200..1>[Gene],[GeneOrganismRelationship]-%20gene%200..1>[Gene],[GeneSubcellularLocalizationRelationship]-%20gene%200..1>[Gene],[IBDAnnotations]-%20genes%200..*>[Gene],[NamedEntity]^-[Gene],[IBDAnnotations],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship],[GeneGeneInteraction]) - -## Identifier prefixes - - * HGNC - * PR - * UniProtKB - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞gene1](geneGeneInteraction__gene1.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene2](geneGeneInteraction__gene2.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneMolecularActivityRelationship2__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneMolecularActivityRelationship__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneOrganismRelationship__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneSubcellularLocalizationRelationship__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞genes](iBDAnnotations__genes.md)* <sub>0..\*</sub> **[Gene](Gene.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/GeneGeneInteraction.md b/projects/ibd/docs/GeneGeneInteraction.md deleted file mode 100644 index 805d01b25..000000000 --- a/projects/ibd/docs/GeneGeneInteraction.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: GeneGeneInteraction - - - - -URI: [gocam:GeneGeneInteraction](http://w3id.org/ontogpt/gocam/GeneGeneInteraction) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Gene]<gene2%200..1-%20[GeneGeneInteraction],[Gene]<gene1%200..1-%20[GeneGeneInteraction],[IBDAnnotations]++-%20gene_gene_interactions%200..*>[GeneGeneInteraction],[CompoundExpression]^-[GeneGeneInteraction],[IBDAnnotations],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Gene]<gene2%200..1-%20[GeneGeneInteraction],[Gene]<gene1%200..1-%20[GeneGeneInteraction],[IBDAnnotations]++-%20gene_gene_interactions%200..*>[GeneGeneInteraction],[CompoundExpression]^-[GeneGeneInteraction],[IBDAnnotations],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_gene_interactions](iBDAnnotations__gene_gene_interactions.md)* <sub>0..\*</sub> **[GeneGeneInteraction](GeneGeneInteraction.md)** - -## Attributes - - -### Own - - * [➞gene1](geneGeneInteraction__gene1.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞gene2](geneGeneInteraction__gene2.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) diff --git a/projects/ibd/docs/GeneLocation.md b/projects/ibd/docs/GeneLocation.md deleted file mode 100644 index d54b4da61..000000000 --- a/projects/ibd/docs/GeneLocation.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Class: GeneLocation - - - - -URI: [gocam:GeneLocation](http://w3id.org/ontogpt/gocam/GeneLocation) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneSubcellularLocalizationRelationship]-%20location%200..1>[GeneLocation|id:string;label(i):string%20%3F],[NamedEntity]^-[GeneLocation],[GeneSubcellularLocalizationRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneSubcellularLocalizationRelationship]-%20location%200..1>[GeneLocation|id:string;label(i):string%20%3F],[NamedEntity]^-[GeneLocation],[GeneSubcellularLocalizationRelationship]) - -## Identifier prefixes - - * GO - * CL - * UBERON - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞location](geneSubcellularLocalizationRelationship__location.md)* <sub>0..1</sub> **[GeneLocation](GeneLocation.md)** - -## Attributes - - -### Own - - * [GeneLocation➞id](GeneLocation_id.md) <sub>1..1</sub> - * Range: [String](types/String.md) - -### Inherited from NamedEntity: - - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/GeneLocationEnum.md b/projects/ibd/docs/GeneLocationEnum.md deleted file mode 100644 index 67626c0d9..000000000 --- a/projects/ibd/docs/GeneLocationEnum.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: GeneLocationEnum - - - - -URI: [gocam:GeneLocationEnum](http://w3id.org/ontogpt/gocam/GeneLocationEnum) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/ibd/docs/GeneLocation_id.md b/projects/ibd/docs/GeneLocation_id.md deleted file mode 100644 index 1357ee5d7..000000000 --- a/projects/ibd/docs/GeneLocation_id.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: id - - - - -URI: [gocam:GeneLocation_id](http://w3id.org/ontogpt/gocam/GeneLocation_id) - - -## Domain and Range - -[GeneLocation](GeneLocation.md) → <sub>1..1</sub> [String](types/String.md) - -## Parents - - * is_a: [➞id](namedEntity__id.md) - -## Children - - -## Used by - - * [GeneLocation](GeneLocation.md) diff --git a/projects/ibd/docs/GeneMolecularActivityRelationship.md b/projects/ibd/docs/GeneMolecularActivityRelationship.md deleted file mode 100644 index d6e7a741d..000000000 --- a/projects/ibd/docs/GeneMolecularActivityRelationship.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: GeneMolecularActivityRelationship - - - - -URI: [gocam:GeneMolecularActivityRelationship](http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[MolecularActivity],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship],[IBDAnnotations]++-%20gene_functions%200..*>[GeneMolecularActivityRelationship],[CompoundExpression]^-[GeneMolecularActivityRelationship],[IBDAnnotations],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[MolecularActivity],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship],[IBDAnnotations]++-%20gene_functions%200..*>[GeneMolecularActivityRelationship],[CompoundExpression]^-[GeneMolecularActivityRelationship],[IBDAnnotations],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_functions](iBDAnnotations__gene_functions.md)* <sub>0..\*</sub> **[GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md)** - -## Attributes - - -### Own - - * [➞gene](geneMolecularActivityRelationship__gene.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md) <sub>0..1</sub> - * Range: [MolecularActivity](MolecularActivity.md) diff --git a/projects/ibd/docs/GeneMolecularActivityRelationship2.md b/projects/ibd/docs/GeneMolecularActivityRelationship2.md deleted file mode 100644 index 395313a4f..000000000 --- a/projects/ibd/docs/GeneMolecularActivityRelationship2.md +++ /dev/null @@ -1,26 +0,0 @@ - -# Class: GeneMolecularActivityRelationship2 - - - - -URI: [gocam:GeneMolecularActivityRelationship2](http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship2) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Molecule],[MolecularActivity],[Molecule]<target%200..1-%20[GeneMolecularActivityRelationship2],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship2],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship2],[CompoundExpression]^-[GeneMolecularActivityRelationship2],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Molecule],[MolecularActivity],[Molecule]<target%200..1-%20[GeneMolecularActivityRelationship2],[MolecularActivity]<molecular_activity%200..1-%20[GeneMolecularActivityRelationship2],[Gene]<gene%200..1-%20[GeneMolecularActivityRelationship2],[CompoundExpression]^-[GeneMolecularActivityRelationship2],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Attributes - - -### Own - - * [➞gene](geneMolecularActivityRelationship2__gene.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship2__molecular_activity.md) <sub>0..1</sub> - * Range: [MolecularActivity](MolecularActivity.md) - * [➞target](geneMolecularActivityRelationship2__target.md) <sub>0..1</sub> - * Range: [Molecule](Molecule.md) diff --git a/projects/ibd/docs/GeneOrganismRelationship.md b/projects/ibd/docs/GeneOrganismRelationship.md deleted file mode 100644 index d5c29e09a..000000000 --- a/projects/ibd/docs/GeneOrganismRelationship.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: GeneOrganismRelationship - - - - -URI: [gocam:GeneOrganismRelationship](http://w3id.org/ontogpt/gocam/GeneOrganismRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Organism],[Organism]<organism%200..1-%20[GeneOrganismRelationship],[Gene]<gene%200..1-%20[GeneOrganismRelationship],[IBDAnnotations]++-%20gene_organisms%200..*>[GeneOrganismRelationship],[CompoundExpression]^-[GeneOrganismRelationship],[IBDAnnotations],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Organism],[Organism]<organism%200..1-%20[GeneOrganismRelationship],[Gene]<gene%200..1-%20[GeneOrganismRelationship],[IBDAnnotations]++-%20gene_organisms%200..*>[GeneOrganismRelationship],[CompoundExpression]^-[GeneOrganismRelationship],[IBDAnnotations],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_organisms](iBDAnnotations__gene_organisms.md)* <sub>0..\*</sub> **[GeneOrganismRelationship](GeneOrganismRelationship.md)** - -## Attributes - - -### Own - - * [➞gene](geneOrganismRelationship__gene.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞organism](geneOrganismRelationship__organism.md) <sub>0..1</sub> - * Range: [Organism](Organism.md) diff --git a/projects/ibd/docs/GeneSubcellularLocalizationRelationship.md b/projects/ibd/docs/GeneSubcellularLocalizationRelationship.md deleted file mode 100644 index c7de454f4..000000000 --- a/projects/ibd/docs/GeneSubcellularLocalizationRelationship.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: GeneSubcellularLocalizationRelationship - - - - -URI: [gocam:GeneSubcellularLocalizationRelationship](http://w3id.org/ontogpt/gocam/GeneSubcellularLocalizationRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneLocation]<location%200..1-%20[GeneSubcellularLocalizationRelationship],[Gene]<gene%200..1-%20[GeneSubcellularLocalizationRelationship],[IBDAnnotations]++-%20gene_localizations%200..*>[GeneSubcellularLocalizationRelationship],[CompoundExpression]^-[GeneSubcellularLocalizationRelationship],[IBDAnnotations],[GeneLocation],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneLocation]<location%200..1-%20[GeneSubcellularLocalizationRelationship],[Gene]<gene%200..1-%20[GeneSubcellularLocalizationRelationship],[IBDAnnotations]++-%20gene_localizations%200..*>[GeneSubcellularLocalizationRelationship],[CompoundExpression]^-[GeneSubcellularLocalizationRelationship],[IBDAnnotations],[GeneLocation],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_localizations](iBDAnnotations__gene_localizations.md)* <sub>0..\*</sub> **[GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md)** - -## Attributes - - -### Own - - * [➞gene](geneSubcellularLocalizationRelationship__gene.md) <sub>0..1</sub> - * Range: [Gene](Gene.md) - * [➞location](geneSubcellularLocalizationRelationship__location.md) <sub>0..1</sub> - * Range: [GeneLocation](GeneLocation.md) diff --git a/projects/ibd/docs/IBDAnnotations.md b/projects/ibd/docs/IBDAnnotations.md deleted file mode 100644 index f37991365..000000000 --- a/projects/ibd/docs/IBDAnnotations.md +++ /dev/null @@ -1,42 +0,0 @@ - -# Class: IBDAnnotations - - - - -URI: [gocam:IBDAnnotations](http://w3id.org/ontogpt/gocam/IBDAnnotations) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Pathway],[Organism],[MolecularActivity],[GeneSubcellularLocalizationRelationship]<gene_localizations%200..*-++[IBDAnnotations],[GeneGeneInteraction]<gene_gene_interactions%200..*-++[IBDAnnotations],[Pathway]<pathways%200..*-%20[IBDAnnotations],[CellularProcess]<cellular_processes%200..*-%20[IBDAnnotations],[GeneMolecularActivityRelationship]<gene_functions%200..*-++[IBDAnnotations],[MolecularActivity]<activities%200..*-%20[IBDAnnotations],[GeneOrganismRelationship]<gene_organisms%200..*-++[IBDAnnotations],[Organism]<organisms%200..*-%20[IBDAnnotations],[Gene]<genes%200..*-%20[IBDAnnotations],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship],[GeneGeneInteraction],[Gene],[CellularProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[Pathway],[Organism],[MolecularActivity],[GeneSubcellularLocalizationRelationship]<gene_localizations%200..*-++[IBDAnnotations],[GeneGeneInteraction]<gene_gene_interactions%200..*-++[IBDAnnotations],[Pathway]<pathways%200..*-%20[IBDAnnotations],[CellularProcess]<cellular_processes%200..*-%20[IBDAnnotations],[GeneMolecularActivityRelationship]<gene_functions%200..*-++[IBDAnnotations],[MolecularActivity]<activities%200..*-%20[IBDAnnotations],[GeneOrganismRelationship]<gene_organisms%200..*-++[IBDAnnotations],[Organism]<organisms%200..*-%20[IBDAnnotations],[Gene]<genes%200..*-%20[IBDAnnotations],[GeneSubcellularLocalizationRelationship],[GeneOrganismRelationship],[GeneMolecularActivityRelationship],[GeneGeneInteraction],[Gene],[CellularProcess]) - -## Attributes - - -### Own - - * [➞genes](iBDAnnotations__genes.md) <sub>0..\*</sub> - * Description: semicolon-separated list of genes - * Range: [Gene](Gene.md) - * [➞organisms](iBDAnnotations__organisms.md) <sub>0..\*</sub> - * Description: semicolon-separated list of organism taxons - * Range: [Organism](Organism.md) - * [➞gene_organisms](iBDAnnotations__gene_organisms.md) <sub>0..\*</sub> - * Range: [GeneOrganismRelationship](GeneOrganismRelationship.md) - * [➞activities](iBDAnnotations__activities.md) <sub>0..\*</sub> - * Description: semicolon-separated list of molecular activities - * Range: [MolecularActivity](MolecularActivity.md) - * [➞gene_functions](iBDAnnotations__gene_functions.md) <sub>0..\*</sub> - * Description: semicolon-separated list of gene to molecular activity relationships - * Range: [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - * [➞cellular_processes](iBDAnnotations__cellular_processes.md) <sub>0..\*</sub> - * Description: semicolon-separated list of cellular processes - * Range: [CellularProcess](CellularProcess.md) - * [➞pathways](iBDAnnotations__pathways.md) <sub>0..\*</sub> - * Description: semicolon-separated list of pathways - * Range: [Pathway](Pathway.md) - * [➞gene_gene_interactions](iBDAnnotations__gene_gene_interactions.md) <sub>0..\*</sub> - * Description: semicolon-separated list of gene to gene interactions - * Range: [GeneGeneInteraction](GeneGeneInteraction.md) - * [➞gene_localizations](iBDAnnotations__gene_localizations.md) <sub>0..\*</sub> - * Description: semicolon-separated list of genes plus their location in the cell; for example, "gene1 / cytoplasm; gene2 / mitochondrion" - * Range: [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) diff --git a/projects/ibd/docs/MolecularActivity.md b/projects/ibd/docs/MolecularActivity.md deleted file mode 100644 index bc4583fba..000000000 --- a/projects/ibd/docs/MolecularActivity.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: MolecularActivity - - - - -URI: [gocam:MolecularActivity](http://w3id.org/ontogpt/gocam/MolecularActivity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneMolecularActivityRelationship2]-%20molecular_activity%200..1>[MolecularActivity|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20molecular_activity%200..1>[MolecularActivity],[IBDAnnotations]-%20activities%200..*>[MolecularActivity],[NamedEntity]^-[MolecularActivity],[IBDAnnotations],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneMolecularActivityRelationship2]-%20molecular_activity%200..1>[MolecularActivity|id(i):string;label(i):string%20%3F],[GeneMolecularActivityRelationship]-%20molecular_activity%200..1>[MolecularActivity],[IBDAnnotations]-%20activities%200..*>[MolecularActivity],[NamedEntity]^-[MolecularActivity],[IBDAnnotations],[GeneMolecularActivityRelationship2],[GeneMolecularActivityRelationship]) - -## Identifier prefixes - - * GO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞molecular_activity](geneMolecularActivityRelationship2__molecular_activity.md)* <sub>0..1</sub> **[MolecularActivity](MolecularActivity.md)** - * **None** *[➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md)* <sub>0..1</sub> **[MolecularActivity](MolecularActivity.md)** - * **None** *[➞activities](iBDAnnotations__activities.md)* <sub>0..\*</sub> **[MolecularActivity](MolecularActivity.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/Molecule.md b/projects/ibd/docs/Molecule.md deleted file mode 100644 index 2dc4c84f4..000000000 --- a/projects/ibd/docs/Molecule.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Molecule - - - - -URI: [gocam:Molecule](http://w3id.org/ontogpt/gocam/Molecule) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneMolecularActivityRelationship2]-%20target%200..1>[Molecule|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Molecule],[GeneMolecularActivityRelationship2])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneMolecularActivityRelationship2]-%20target%200..1>[Molecule|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Molecule],[GeneMolecularActivityRelationship2]) - -## Identifier prefixes - - * CHEBI - * PR - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞target](geneMolecularActivityRelationship2__target.md)* <sub>0..1</sub> **[Molecule](Molecule.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/NamedEntity.md b/projects/ibd/docs/NamedEntity.md deleted file mode 100644 index 3896f74ca..000000000 --- a/projects/ibd/docs/NamedEntity.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [gocam:NamedEntity](http://w3id.org/ontogpt/gocam/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Pathway],[Organism],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Pathway],[NamedEntity]^-[Organism],[NamedEntity]^-[Molecule],[NamedEntity]^-[MolecularActivity],[NamedEntity]^-[GeneLocation],[NamedEntity]^-[Gene],[NamedEntity]^-[CellularProcess],[Triple],[Molecule],[MolecularActivity],[GeneLocation],[Gene],[CellularProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Pathway],[Organism],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Pathway],[NamedEntity]^-[Organism],[NamedEntity]^-[Molecule],[NamedEntity]^-[MolecularActivity],[NamedEntity]^-[GeneLocation],[NamedEntity]^-[Gene],[NamedEntity]^-[CellularProcess],[Triple],[Molecule],[MolecularActivity],[GeneLocation],[Gene],[CellularProcess]) - -## Children - - * [CellularProcess](CellularProcess.md) - * [Gene](Gene.md) - * [GeneLocation](GeneLocation.md) - * [MolecularActivity](MolecularActivity.md) - * [Molecule](Molecule.md) - * [Organism](Organism.md) - * [Pathway](Pathway.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/NullDataOptions.md b/projects/ibd/docs/NullDataOptions.md deleted file mode 100644 index abbb7e68a..000000000 --- a/projects/ibd/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [gocam:NullDataOptions](http://w3id.org/ontogpt/gocam/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/ibd/docs/Organism.md b/projects/ibd/docs/Organism.md deleted file mode 100644 index c9826ae6b..000000000 --- a/projects/ibd/docs/Organism.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: Organism - - - - -URI: [gocam:Organism](http://w3id.org/ontogpt/gocam/Organism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneOrganismRelationship]-%20organism%200..1>[Organism|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20organisms%200..*>[Organism],[NamedEntity]^-[Organism],[NamedEntity],[IBDAnnotations],[GeneOrganismRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneOrganismRelationship]-%20organism%200..1>[Organism|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20organisms%200..*>[Organism],[NamedEntity]^-[Organism],[NamedEntity],[IBDAnnotations],[GeneOrganismRelationship]) - -## Identifier prefixes - - * NCBITaxon - * EFO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞organism](geneOrganismRelationship__organism.md)* <sub>0..1</sub> **[Organism](Organism.md)** - * **None** *[➞organisms](iBDAnnotations__organisms.md)* <sub>0..\*</sub> **[Organism](Organism.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/Pathway.md b/projects/ibd/docs/Pathway.md deleted file mode 100644 index 3028f7bf2..000000000 --- a/projects/ibd/docs/Pathway.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Pathway - - - - -URI: [gocam:Pathway](http://w3id.org/ontogpt/gocam/Pathway) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[IBDAnnotations]-%20pathways%200..*>[Pathway|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Pathway],[NamedEntity],[IBDAnnotations])](https://yuml.me/diagram/nofunky;dir:TB/class/[IBDAnnotations]-%20pathways%200..*>[Pathway|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Pathway],[NamedEntity],[IBDAnnotations]) - -## Identifier prefixes - - * GO - * PW - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞pathways](iBDAnnotations__pathways.md)* <sub>0..\*</sub> **[Pathway](Pathway.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/Publication.md b/projects/ibd/docs/Publication.md deleted file mode 100644 index 64d87f10d..000000000 --- a/projects/ibd/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [gocam:Publication](http://w3id.org/ontogpt/gocam/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/RelationshipType.md b/projects/ibd/docs/RelationshipType.md deleted file mode 100644 index ea382170c..000000000 --- a/projects/ibd/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [gocam:RelationshipType](http://w3id.org/ontogpt/gocam/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd/docs/TextWithTriples.md b/projects/ibd/docs/TextWithTriples.md deleted file mode 100644 index 77200b9c3..000000000 --- a/projects/ibd/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [gocam:TextWithTriples](http://w3id.org/ontogpt/gocam/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/ibd/docs/Triple.md b/projects/ibd/docs/Triple.md deleted file mode 100644 index 77c3e9483..000000000 --- a/projects/ibd/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [gocam:Triple](http://w3id.org/ontogpt/gocam/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/ibd/docs/annotatorResult__object_id.md b/projects/ibd/docs/annotatorResult__object_id.md deleted file mode 100644 index 77a3040ba..000000000 --- a/projects/ibd/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [gocam:annotatorResult__object_id](http://w3id.org/ontogpt/gocam/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ibd/docs/annotatorResult__object_text.md b/projects/ibd/docs/annotatorResult__object_text.md deleted file mode 100644 index 2869435f2..000000000 --- a/projects/ibd/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [gocam:annotatorResult__object_text](http://w3id.org/ontogpt/gocam/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ibd/docs/annotatorResult__subject_text.md b/projects/ibd/docs/annotatorResult__subject_text.md deleted file mode 100644 index 6f92b2c48..000000000 --- a/projects/ibd/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [gocam:annotatorResult__subject_text](http://w3id.org/ontogpt/gocam/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ibd/docs/extractionResult__extracted_object.md b/projects/ibd/docs/extractionResult__extracted_object.md deleted file mode 100644 index 8e46f1540..000000000 --- a/projects/ibd/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [gocam:extractionResult__extracted_object](http://w3id.org/ontogpt/gocam/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd/docs/extractionResult__input_id.md b/projects/ibd/docs/extractionResult__input_id.md deleted file mode 100644 index d667d9cc3..000000000 --- a/projects/ibd/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [gocam:extractionResult__input_id](http://w3id.org/ontogpt/gocam/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd/docs/extractionResult__input_text.md b/projects/ibd/docs/extractionResult__input_text.md deleted file mode 100644 index 5d130aab5..000000000 --- a/projects/ibd/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [gocam:extractionResult__input_text](http://w3id.org/ontogpt/gocam/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd/docs/extractionResult__input_title.md b/projects/ibd/docs/extractionResult__input_title.md deleted file mode 100644 index 80c0a0585..000000000 --- a/projects/ibd/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [gocam:extractionResult__input_title](http://w3id.org/ontogpt/gocam/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd/docs/extractionResult__named_entities.md b/projects/ibd/docs/extractionResult__named_entities.md deleted file mode 100644 index 6680295e3..000000000 --- a/projects/ibd/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [gocam:extractionResult__named_entities](http://w3id.org/ontogpt/gocam/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd/docs/extractionResult__prompt.md b/projects/ibd/docs/extractionResult__prompt.md deleted file mode 100644 index 0bc5b4d86..000000000 --- a/projects/ibd/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [gocam:extractionResult__prompt](http://w3id.org/ontogpt/gocam/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd/docs/extractionResult__raw_completion_output.md b/projects/ibd/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index d5b8ad15b..000000000 --- a/projects/ibd/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [gocam:extractionResult__raw_completion_output](http://w3id.org/ontogpt/gocam/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd/docs/geneGeneInteraction__gene1.md b/projects/ibd/docs/geneGeneInteraction__gene1.md deleted file mode 100644 index 25ff5d3e1..000000000 --- a/projects/ibd/docs/geneGeneInteraction__gene1.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene1 - - - - -URI: [gocam:geneGeneInteraction__gene1](http://w3id.org/ontogpt/gocam/geneGeneInteraction__gene1) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneGeneInteraction](GeneGeneInteraction.md) diff --git a/projects/ibd/docs/geneGeneInteraction__gene2.md b/projects/ibd/docs/geneGeneInteraction__gene2.md deleted file mode 100644 index 8ad830681..000000000 --- a/projects/ibd/docs/geneGeneInteraction__gene2.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene2 - - - - -URI: [gocam:geneGeneInteraction__gene2](http://w3id.org/ontogpt/gocam/geneGeneInteraction__gene2) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneGeneInteraction](GeneGeneInteraction.md) diff --git a/projects/ibd/docs/geneMolecularActivityRelationship2__gene.md b/projects/ibd/docs/geneMolecularActivityRelationship2__gene.md deleted file mode 100644 index 29e3876af..000000000 --- a/projects/ibd/docs/geneMolecularActivityRelationship2__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [gocam:geneMolecularActivityRelationship2__gene](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship2__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) diff --git a/projects/ibd/docs/geneMolecularActivityRelationship2__molecular_activity.md b/projects/ibd/docs/geneMolecularActivityRelationship2__molecular_activity.md deleted file mode 100644 index db47a4345..000000000 --- a/projects/ibd/docs/geneMolecularActivityRelationship2__molecular_activity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: molecular_activity - - - - -URI: [gocam:geneMolecularActivityRelationship2__molecular_activity](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship2__molecular_activity) - - -## Domain and Range - -None → <sub>0..1</sub> [MolecularActivity](MolecularActivity.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) diff --git a/projects/ibd/docs/geneMolecularActivityRelationship2__target.md b/projects/ibd/docs/geneMolecularActivityRelationship2__target.md deleted file mode 100644 index bb68d8cef..000000000 --- a/projects/ibd/docs/geneMolecularActivityRelationship2__target.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: target - - - - -URI: [gocam:geneMolecularActivityRelationship2__target](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship2__target) - - -## Domain and Range - -None → <sub>0..1</sub> [Molecule](Molecule.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) diff --git a/projects/ibd/docs/geneMolecularActivityRelationship__gene.md b/projects/ibd/docs/geneMolecularActivityRelationship__gene.md deleted file mode 100644 index e4df4fa20..000000000 --- a/projects/ibd/docs/geneMolecularActivityRelationship__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [gocam:geneMolecularActivityRelationship__gene](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) diff --git a/projects/ibd/docs/geneMolecularActivityRelationship__molecular_activity.md b/projects/ibd/docs/geneMolecularActivityRelationship__molecular_activity.md deleted file mode 100644 index 42577e0a6..000000000 --- a/projects/ibd/docs/geneMolecularActivityRelationship__molecular_activity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: molecular_activity - - - - -URI: [gocam:geneMolecularActivityRelationship__molecular_activity](http://w3id.org/ontogpt/gocam/geneMolecularActivityRelationship__molecular_activity) - - -## Domain and Range - -None → <sub>0..1</sub> [MolecularActivity](MolecularActivity.md) - -## Parents - - -## Children - - -## Used by - - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) diff --git a/projects/ibd/docs/geneOrganismRelationship__gene.md b/projects/ibd/docs/geneOrganismRelationship__gene.md deleted file mode 100644 index 7071e06cd..000000000 --- a/projects/ibd/docs/geneOrganismRelationship__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [gocam:geneOrganismRelationship__gene](http://w3id.org/ontogpt/gocam/geneOrganismRelationship__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneOrganismRelationship](GeneOrganismRelationship.md) diff --git a/projects/ibd/docs/geneOrganismRelationship__organism.md b/projects/ibd/docs/geneOrganismRelationship__organism.md deleted file mode 100644 index 80ad6c95a..000000000 --- a/projects/ibd/docs/geneOrganismRelationship__organism.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: organism - - - - -URI: [gocam:geneOrganismRelationship__organism](http://w3id.org/ontogpt/gocam/geneOrganismRelationship__organism) - - -## Domain and Range - -None → <sub>0..1</sub> [Organism](Organism.md) - -## Parents - - -## Children - - -## Used by - - * [GeneOrganismRelationship](GeneOrganismRelationship.md) diff --git a/projects/ibd/docs/geneSubcellularLocalizationRelationship__gene.md b/projects/ibd/docs/geneSubcellularLocalizationRelationship__gene.md deleted file mode 100644 index 719048841..000000000 --- a/projects/ibd/docs/geneSubcellularLocalizationRelationship__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - - - -URI: [gocam:geneSubcellularLocalizationRelationship__gene](http://w3id.org/ontogpt/gocam/geneSubcellularLocalizationRelationship__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) diff --git a/projects/ibd/docs/geneSubcellularLocalizationRelationship__location.md b/projects/ibd/docs/geneSubcellularLocalizationRelationship__location.md deleted file mode 100644 index c5e53c56a..000000000 --- a/projects/ibd/docs/geneSubcellularLocalizationRelationship__location.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: location - - - - -URI: [gocam:geneSubcellularLocalizationRelationship__location](http://w3id.org/ontogpt/gocam/geneSubcellularLocalizationRelationship__location) - - -## Domain and Range - -None → <sub>0..1</sub> [GeneLocation](GeneLocation.md) - -## Parents - - -## Children - - -## Used by - - * [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) diff --git a/projects/ibd/docs/iBDAnnotations__activities.md b/projects/ibd/docs/iBDAnnotations__activities.md deleted file mode 100644 index e2c0792b4..000000000 --- a/projects/ibd/docs/iBDAnnotations__activities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: activities - - -semicolon-separated list of molecular activities - -URI: [gocam:iBDAnnotations__activities](http://w3id.org/ontogpt/gocam/iBDAnnotations__activities) - - -## Domain and Range - -None → <sub>0..\*</sub> [MolecularActivity](MolecularActivity.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/iBDAnnotations__cellular_processes.md b/projects/ibd/docs/iBDAnnotations__cellular_processes.md deleted file mode 100644 index 13b6e9122..000000000 --- a/projects/ibd/docs/iBDAnnotations__cellular_processes.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: cellular_processes - - -semicolon-separated list of cellular processes - -URI: [gocam:iBDAnnotations__cellular_processes](http://w3id.org/ontogpt/gocam/iBDAnnotations__cellular_processes) - - -## Domain and Range - -None → <sub>0..\*</sub> [CellularProcess](CellularProcess.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/iBDAnnotations__gene_functions.md b/projects/ibd/docs/iBDAnnotations__gene_functions.md deleted file mode 100644 index 3d7d3d04e..000000000 --- a/projects/ibd/docs/iBDAnnotations__gene_functions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_functions - - -semicolon-separated list of gene to molecular activity relationships - -URI: [gocam:iBDAnnotations__gene_functions](http://w3id.org/ontogpt/gocam/iBDAnnotations__gene_functions) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/iBDAnnotations__gene_gene_interactions.md b/projects/ibd/docs/iBDAnnotations__gene_gene_interactions.md deleted file mode 100644 index c553ca666..000000000 --- a/projects/ibd/docs/iBDAnnotations__gene_gene_interactions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_gene_interactions - - -semicolon-separated list of gene to gene interactions - -URI: [gocam:iBDAnnotations__gene_gene_interactions](http://w3id.org/ontogpt/gocam/iBDAnnotations__gene_gene_interactions) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneGeneInteraction](GeneGeneInteraction.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/iBDAnnotations__gene_localizations.md b/projects/ibd/docs/iBDAnnotations__gene_localizations.md deleted file mode 100644 index 405c87867..000000000 --- a/projects/ibd/docs/iBDAnnotations__gene_localizations.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_localizations - - -semicolon-separated list of genes plus their location in the cell; for example, "gene1 / cytoplasm; gene2 / mitochondrion" - -URI: [gocam:iBDAnnotations__gene_localizations](http://w3id.org/ontogpt/gocam/iBDAnnotations__gene_localizations) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/iBDAnnotations__gene_organisms.md b/projects/ibd/docs/iBDAnnotations__gene_organisms.md deleted file mode 100644 index fc53b0518..000000000 --- a/projects/ibd/docs/iBDAnnotations__gene_organisms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_organisms - - - - -URI: [gocam:iBDAnnotations__gene_organisms](http://w3id.org/ontogpt/gocam/iBDAnnotations__gene_organisms) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneOrganismRelationship](GeneOrganismRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/iBDAnnotations__genes.md b/projects/ibd/docs/iBDAnnotations__genes.md deleted file mode 100644 index beea5579f..000000000 --- a/projects/ibd/docs/iBDAnnotations__genes.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: genes - - -semicolon-separated list of genes - -URI: [gocam:iBDAnnotations__genes](http://w3id.org/ontogpt/gocam/iBDAnnotations__genes) - - -## Domain and Range - -None → <sub>0..\*</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/iBDAnnotations__organisms.md b/projects/ibd/docs/iBDAnnotations__organisms.md deleted file mode 100644 index 60d4434e7..000000000 --- a/projects/ibd/docs/iBDAnnotations__organisms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: organisms - - -semicolon-separated list of organism taxons - -URI: [gocam:iBDAnnotations__organisms](http://w3id.org/ontogpt/gocam/iBDAnnotations__organisms) - - -## Domain and Range - -None → <sub>0..\*</sub> [Organism](Organism.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/iBDAnnotations__pathways.md b/projects/ibd/docs/iBDAnnotations__pathways.md deleted file mode 100644 index 9986dd470..000000000 --- a/projects/ibd/docs/iBDAnnotations__pathways.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: pathways - - -semicolon-separated list of pathways - -URI: [gocam:iBDAnnotations__pathways](http://w3id.org/ontogpt/gocam/iBDAnnotations__pathways) - - -## Domain and Range - -None → <sub>0..\*</sub> [Pathway](Pathway.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd/docs/ibd.md b/projects/ibd/docs/ibd.md deleted file mode 100644 index 4ecc2e294..000000000 --- a/projects/ibd/docs/ibd.md +++ /dev/null @@ -1,140 +0,0 @@ - -# gocam-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for GO-CAMs - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [GeneGeneInteraction](GeneGeneInteraction.md) - * [GeneMolecularActivityRelationship](GeneMolecularActivityRelationship.md) - * [GeneMolecularActivityRelationship2](GeneMolecularActivityRelationship2.md) - * [GeneOrganismRelationship](GeneOrganismRelationship.md) - * [GeneSubcellularLocalizationRelationship](GeneSubcellularLocalizationRelationship.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [IBDAnnotations](IBDAnnotations.md) - * [NamedEntity](NamedEntity.md) - * [CellularProcess](CellularProcess.md) - * [Gene](Gene.md) - * [GeneLocation](GeneLocation.md) - * [MolecularActivity](MolecularActivity.md) - * [Molecule](Molecule.md) - * [Organism](Organism.md) - * [Pathway](Pathway.md) - * [RelationshipType](RelationshipType.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞gene1](geneGeneInteraction__gene1.md) - * [➞gene2](geneGeneInteraction__gene2.md) - * [➞gene](geneMolecularActivityRelationship2__gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship2__molecular_activity.md) - * [➞target](geneMolecularActivityRelationship2__target.md) - * [➞gene](geneMolecularActivityRelationship__gene.md) - * [➞molecular_activity](geneMolecularActivityRelationship__molecular_activity.md) - * [➞gene](geneOrganismRelationship__gene.md) - * [➞organism](geneOrganismRelationship__organism.md) - * [➞gene](geneSubcellularLocalizationRelationship__gene.md) - * [➞location](geneSubcellularLocalizationRelationship__location.md) - * [➞activities](iBDAnnotations__activities.md) - semicolon-separated list of molecular activities - * [➞cellular_processes](iBDAnnotations__cellular_processes.md) - semicolon-separated list of cellular processes - * [➞gene_functions](iBDAnnotations__gene_functions.md) - semicolon-separated list of gene to molecular activity relationships - * [➞gene_gene_interactions](iBDAnnotations__gene_gene_interactions.md) - semicolon-separated list of gene to gene interactions - * [➞gene_localizations](iBDAnnotations__gene_localizations.md) - semicolon-separated list of genes plus their location in the cell; for example, "gene1 / cytoplasm; gene2 / mitochondrion" - * [➞gene_organisms](iBDAnnotations__gene_organisms.md) - * [➞genes](iBDAnnotations__genes.md) - semicolon-separated list of genes - * [➞organisms](iBDAnnotations__organisms.md) - semicolon-separated list of organism taxons - * [➞pathways](iBDAnnotations__pathways.md) - semicolon-separated list of pathways - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [GeneLocation➞id](GeneLocation_id.md) - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [CellType](CellType.md) - * [GOCellComponentType](GOCellComponentType.md) - * [GeneLocationEnum](GeneLocationEnum.md) - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/ibd/docs/namedEntity__id.md b/projects/ibd/docs/namedEntity__id.md deleted file mode 100644 index 0555a9f73..000000000 --- a/projects/ibd/docs/namedEntity__id.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [gocam:namedEntity__id](http://w3id.org/ontogpt/gocam/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - * [GeneLocation➞id](GeneLocation_id.md) - -## Used by - - * [CellularProcess](CellularProcess.md) - * [Gene](Gene.md) - * [MolecularActivity](MolecularActivity.md) - * [Molecule](Molecule.md) - * [NamedEntity](NamedEntity.md) - * [Organism](Organism.md) - * [Pathway](Pathway.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/ibd/docs/namedEntity__label.md b/projects/ibd/docs/namedEntity__label.md deleted file mode 100644 index 2b599b1cc..000000000 --- a/projects/ibd/docs/namedEntity__label.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [gocam:namedEntity__label](http://w3id.org/ontogpt/gocam/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [CellularProcess](CellularProcess.md) - * [Gene](Gene.md) - * [GeneLocation](GeneLocation.md) - * [MolecularActivity](MolecularActivity.md) - * [Molecule](Molecule.md) - * [NamedEntity](NamedEntity.md) - * [Organism](Organism.md) - * [Pathway](Pathway.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/ibd/docs/publication__abstract.md b/projects/ibd/docs/publication__abstract.md deleted file mode 100644 index dd434bed1..000000000 --- a/projects/ibd/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [gocam:publication__abstract](http://w3id.org/ontogpt/gocam/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd/docs/publication__combined_text.md b/projects/ibd/docs/publication__combined_text.md deleted file mode 100644 index 128ca7aed..000000000 --- a/projects/ibd/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [gocam:publication__combined_text](http://w3id.org/ontogpt/gocam/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd/docs/publication__full_text.md b/projects/ibd/docs/publication__full_text.md deleted file mode 100644 index be255126c..000000000 --- a/projects/ibd/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [gocam:publication__full_text](http://w3id.org/ontogpt/gocam/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd/docs/publication__id.md b/projects/ibd/docs/publication__id.md deleted file mode 100644 index 583585698..000000000 --- a/projects/ibd/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [gocam:publication__id](http://w3id.org/ontogpt/gocam/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd/docs/publication__title.md b/projects/ibd/docs/publication__title.md deleted file mode 100644 index af7b52d3f..000000000 --- a/projects/ibd/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [gocam:publication__title](http://w3id.org/ontogpt/gocam/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd/docs/textWithTriples__publication.md b/projects/ibd/docs/textWithTriples__publication.md deleted file mode 100644 index f2480d2c2..000000000 --- a/projects/ibd/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [gocam:textWithTriples__publication](http://w3id.org/ontogpt/gocam/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ibd/docs/textWithTriples__triples.md b/projects/ibd/docs/textWithTriples__triples.md deleted file mode 100644 index 8fe102100..000000000 --- a/projects/ibd/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [gocam:textWithTriples__triples](http://w3id.org/ontogpt/gocam/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ibd/docs/triple__object.md b/projects/ibd/docs/triple__object.md deleted file mode 100644 index 38e4c4c25..000000000 --- a/projects/ibd/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [gocam:triple__object](http://w3id.org/ontogpt/gocam/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd/docs/triple__object_qualifier.md b/projects/ibd/docs/triple__object_qualifier.md deleted file mode 100644 index 21bae818d..000000000 --- a/projects/ibd/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [gocam:triple__object_qualifier](http://w3id.org/ontogpt/gocam/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd/docs/triple__predicate.md b/projects/ibd/docs/triple__predicate.md deleted file mode 100644 index 3c7c729c3..000000000 --- a/projects/ibd/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [gocam:triple__predicate](http://w3id.org/ontogpt/gocam/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd/docs/triple__qualifier.md b/projects/ibd/docs/triple__qualifier.md deleted file mode 100644 index 7f62d89e8..000000000 --- a/projects/ibd/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [gocam:triple__qualifier](http://w3id.org/ontogpt/gocam/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd/docs/triple__subject.md b/projects/ibd/docs/triple__subject.md deleted file mode 100644 index 9b9ece18a..000000000 --- a/projects/ibd/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [gocam:triple__subject](http://w3id.org/ontogpt/gocam/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd/docs/triple__subject_qualifier.md b/projects/ibd/docs/triple__subject_qualifier.md deleted file mode 100644 index 588c54157..000000000 --- a/projects/ibd/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [gocam:triple__subject_qualifier](http://w3id.org/ontogpt/gocam/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd/docs/types/Boolean.md b/projects/ibd/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/ibd/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/ibd/docs/types/Curie.md b/projects/ibd/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/ibd/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/ibd/docs/types/Date.md b/projects/ibd/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/ibd/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/ibd/docs/types/DateOrDatetime.md b/projects/ibd/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/ibd/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ibd/docs/types/Datetime.md b/projects/ibd/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/ibd/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/ibd/docs/types/Decimal.md b/projects/ibd/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/ibd/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/ibd/docs/types/Double.md b/projects/ibd/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/ibd/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/ibd/docs/types/Float.md b/projects/ibd/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/ibd/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/ibd/docs/types/Integer.md b/projects/ibd/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/ibd/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/ibd/docs/types/Jsonpath.md b/projects/ibd/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/ibd/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ibd/docs/types/Jsonpointer.md b/projects/ibd/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/ibd/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ibd/docs/types/Ncname.md b/projects/ibd/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/ibd/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/ibd/docs/types/Nodeidentifier.md b/projects/ibd/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/ibd/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/ibd/docs/types/Objectidentifier.md b/projects/ibd/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/ibd/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/ibd/docs/types/Sparqlpath.md b/projects/ibd/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/ibd/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ibd/docs/types/String.md b/projects/ibd/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/ibd/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/ibd/docs/types/Time.md b/projects/ibd/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/ibd/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/ibd/docs/types/Uri.md b/projects/ibd/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/ibd/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/ibd/docs/types/Uriorcurie.md b/projects/ibd/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/ibd/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/ibd/excel/ibd.xlsx b/projects/ibd/excel/ibd.xlsx deleted file mode 100644 index 59ed7d9716133b2367279a224ebf4f0dd05b59eb..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 13542 zcmeHuWmFXE+BV&t(jX}e-Q6vrbhm_bBi-GlbazUJNQZPtcSx#)bbSM!ecbY~&%56r z?>c|>ux4hl7SF{q*PYk>JR>g+4uJsz0s;flrwpwkrrw6&1N^NL_(TCd4Xq61ZLO^B z==H3v>6|UhWg=wY+Zj+qZl$&tES2_&8Hp#dm-}2L*x8~Cg&qB`+!Wd(=Xe$w!WuC@ zsdkb&u?BSJd!Y7-gVe%{bqJ3a;)s*unyL~C47r4&&lq=-Rp9l2>ta4<9!kC<*sI~% 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a/projects/ibd/graphql/ibd.graphql +++ /dev/null @@ -1,149 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type CellularProcess - { - id: String! - label: String - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Gene - { - id: String! - label: String - } - -type GeneGeneInteraction - { - gene1: Gene - gene2: Gene - } - -type GeneLocation - { - label: String - id: String! - } - -type GeneMolecularActivityRelationship - { - gene: Gene - molecularActivity: MolecularActivity - } - -type GeneMolecularActivityRelationship2 - { - gene: Gene - molecularActivity: MolecularActivity - target: Molecule - } - -type GeneOrganismRelationship - { - gene: Gene - organism: Organism - } - -type GeneSubcellularLocalizationRelationship - { - gene: Gene - location: GeneLocation - } - -type IBDAnnotations - { - genes: [Gene] - organisms: [Organism] - geneOrganisms: [GeneOrganismRelationship] - activities: [MolecularActivity] - geneFunctions: [GeneMolecularActivityRelationship] - cellularProcesses: [CellularProcess] - pathways: [Pathway] - geneGeneInteractions: [GeneGeneInteraction] - geneLocalizations: [GeneSubcellularLocalizationRelationship] - } - -type MolecularActivity - { - id: String! - label: String - } - -type Molecule - { - id: String! - label: String - } - -interface NamedEntity - { - id: String! - label: String - } - -type Organism - { - id: String! - label: String - } - -type Pathway - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/ibd/ibd.py b/projects/ibd/ibd.py deleted file mode 100644 index 2e865e160..000000000 --- a/projects/ibd/ibd.py +++ /dev/null @@ -1,794 +0,0 @@ -# Auto generated from ibd.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:54:16 -# Schema: gocam-template -# -# id: http://w3id.org/ontogpt/gocam -# description: A template for GO-CAMs -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CHEBI = CurieNamespace('CHEBI', 'http://example.org/UNKNOWN/CHEBI/') -CL = CurieNamespace('CL', 'http://purl.obolibrary.org/obo/CL_') -EFO = CurieNamespace('EFO', 'http://example.org/UNKNOWN/EFO/') -GO = CurieNamespace('GO', 'http://purl.obolibrary.org/obo/GO_') -HGNC = CurieNamespace('HGNC', 'http://example.org/UNKNOWN/HGNC/') -NCBITAXON = CurieNamespace('NCBITaxon', 'http://example.org/UNKNOWN/NCBITaxon/') -PR = CurieNamespace('PR', 'http://example.org/UNKNOWN/PR/') -PW = CurieNamespace('PW', 'http://example.org/UNKNOWN/PW/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -UBERON = CurieNamespace('UBERON', 'http://example.org/UNKNOWN/UBERON/') -UNIPROTKB = CurieNamespace('UniProtKB', 'http://example.org/UNKNOWN/UniProtKB/') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -GOCAM = CurieNamespace('gocam', 'http://w3id.org/ontogpt/gocam/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = GOCAM - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class GeneId(NamedEntityId): - pass - - -class PathwayId(NamedEntityId): - pass - - -class CellularProcessId(NamedEntityId): - pass - - -class MolecularActivityId(NamedEntityId): - pass - - -class GeneLocationId(NamedEntityId): - pass - - -class OrganismId(NamedEntityId): - pass - - -class MoleculeId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class IBDAnnotations(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.IBDAnnotations - class_class_curie: ClassVar[str] = "gocam:IBDAnnotations" - class_name: ClassVar[str] = "IBDAnnotations" - class_model_uri: ClassVar[URIRef] = GOCAM.IBDAnnotations - - genes: Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]] = empty_list() - organisms: Optional[Union[Union[str, OrganismId], List[Union[str, OrganismId]]]] = empty_list() - gene_organisms: Optional[Union[Union[dict, "GeneOrganismRelationship"], List[Union[dict, "GeneOrganismRelationship"]]]] = empty_list() - activities: Optional[Union[Union[str, MolecularActivityId], List[Union[str, MolecularActivityId]]]] = empty_list() - gene_functions: Optional[Union[Union[dict, "GeneMolecularActivityRelationship"], List[Union[dict, "GeneMolecularActivityRelationship"]]]] = empty_list() - cellular_processes: Optional[Union[Union[str, CellularProcessId], List[Union[str, CellularProcessId]]]] = empty_list() - pathways: Optional[Union[Union[str, PathwayId], List[Union[str, PathwayId]]]] = empty_list() - gene_gene_interactions: Optional[Union[Union[dict, "GeneGeneInteraction"], List[Union[dict, "GeneGeneInteraction"]]]] = empty_list() - gene_localizations: Optional[Union[Union[dict, "GeneSubcellularLocalizationRelationship"], List[Union[dict, "GeneSubcellularLocalizationRelationship"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.genes, list): - self.genes = [self.genes] if self.genes is not None else [] - self.genes = [v if isinstance(v, GeneId) else GeneId(v) for v in self.genes] - - if not isinstance(self.organisms, list): - self.organisms = [self.organisms] if self.organisms is not None else [] - self.organisms = [v if isinstance(v, OrganismId) else OrganismId(v) for v in self.organisms] - - if not isinstance(self.gene_organisms, list): - self.gene_organisms = [self.gene_organisms] if self.gene_organisms is not None else [] - self.gene_organisms = [v if isinstance(v, GeneOrganismRelationship) else GeneOrganismRelationship(**as_dict(v)) for v in self.gene_organisms] - - if not isinstance(self.activities, list): - self.activities = [self.activities] if self.activities is not None else [] - self.activities = [v if isinstance(v, MolecularActivityId) else MolecularActivityId(v) for v in self.activities] - - if not isinstance(self.gene_functions, list): - self.gene_functions = [self.gene_functions] if self.gene_functions is not None else [] - self.gene_functions = [v if isinstance(v, GeneMolecularActivityRelationship) else GeneMolecularActivityRelationship(**as_dict(v)) for v in self.gene_functions] - - if not isinstance(self.cellular_processes, list): - self.cellular_processes = [self.cellular_processes] if self.cellular_processes is not None else [] - self.cellular_processes = [v if isinstance(v, CellularProcessId) else CellularProcessId(v) for v in self.cellular_processes] - - if not isinstance(self.pathways, list): - self.pathways = [self.pathways] if self.pathways is not None else [] - self.pathways = [v if isinstance(v, PathwayId) else PathwayId(v) for v in self.pathways] - - if not isinstance(self.gene_gene_interactions, list): - self.gene_gene_interactions = [self.gene_gene_interactions] if self.gene_gene_interactions is not None else [] - self.gene_gene_interactions = [v if isinstance(v, GeneGeneInteraction) else GeneGeneInteraction(**as_dict(v)) for v in self.gene_gene_interactions] - - if not isinstance(self.gene_localizations, list): - self.gene_localizations = [self.gene_localizations] if self.gene_localizations is not None else [] - self.gene_localizations = [v if isinstance(v, GeneSubcellularLocalizationRelationship) else GeneSubcellularLocalizationRelationship(**as_dict(v)) for v in self.gene_localizations] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = GOCAM.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = GOCAM.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.Gene - class_class_curie: ClassVar[str] = "gocam:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = GOCAM.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Pathway(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.Pathway - class_class_curie: ClassVar[str] = "gocam:Pathway" - class_name: ClassVar[str] = "Pathway" - class_model_uri: ClassVar[URIRef] = GOCAM.Pathway - - id: Union[str, PathwayId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, PathwayId): - self.id = PathwayId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class CellularProcess(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.CellularProcess - class_class_curie: ClassVar[str] = "gocam:CellularProcess" - class_name: ClassVar[str] = "CellularProcess" - class_model_uri: ClassVar[URIRef] = GOCAM.CellularProcess - - id: Union[str, CellularProcessId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, CellularProcessId): - self.id = CellularProcessId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class MolecularActivity(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.MolecularActivity - class_class_curie: ClassVar[str] = "gocam:MolecularActivity" - class_name: ClassVar[str] = "MolecularActivity" - class_model_uri: ClassVar[URIRef] = GOCAM.MolecularActivity - - id: Union[str, MolecularActivityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MolecularActivityId): - self.id = MolecularActivityId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneLocation(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneLocation - class_class_curie: ClassVar[str] = "gocam:GeneLocation" - class_name: ClassVar[str] = "GeneLocation" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneLocation - - id: Union[str, GeneLocationId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneLocationId): - self.id = GeneLocationId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Organism(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.Organism - class_class_curie: ClassVar[str] = "gocam:Organism" - class_name: ClassVar[str] = "Organism" - class_model_uri: ClassVar[URIRef] = GOCAM.Organism - - id: Union[str, OrganismId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OrganismId): - self.id = OrganismId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Molecule(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.Molecule - class_class_curie: ClassVar[str] = "gocam:Molecule" - class_name: ClassVar[str] = "Molecule" - class_model_uri: ClassVar[URIRef] = GOCAM.Molecule - - id: Union[str, MoleculeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MoleculeId): - self.id = MoleculeId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = GOCAM.CompoundExpression - - -@dataclass -class GeneOrganismRelationship(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneOrganismRelationship - class_class_curie: ClassVar[str] = "gocam:GeneOrganismRelationship" - class_name: ClassVar[str] = "GeneOrganismRelationship" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneOrganismRelationship - - gene: Optional[Union[str, GeneId]] = None - organism: Optional[Union[str, OrganismId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.organism is not None and not isinstance(self.organism, OrganismId): - self.organism = OrganismId(self.organism) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneMolecularActivityRelationship(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneMolecularActivityRelationship - class_class_curie: ClassVar[str] = "gocam:GeneMolecularActivityRelationship" - class_name: ClassVar[str] = "GeneMolecularActivityRelationship" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneMolecularActivityRelationship - - gene: Optional[Union[str, GeneId]] = None - molecular_activity: Optional[Union[str, MolecularActivityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.molecular_activity is not None and not isinstance(self.molecular_activity, MolecularActivityId): - self.molecular_activity = MolecularActivityId(self.molecular_activity) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneMolecularActivityRelationship2(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneMolecularActivityRelationship2 - class_class_curie: ClassVar[str] = "gocam:GeneMolecularActivityRelationship2" - class_name: ClassVar[str] = "GeneMolecularActivityRelationship2" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneMolecularActivityRelationship2 - - gene: Optional[Union[str, GeneId]] = None - molecular_activity: Optional[Union[str, MolecularActivityId]] = None - target: Optional[Union[str, MoleculeId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.molecular_activity is not None and not isinstance(self.molecular_activity, MolecularActivityId): - self.molecular_activity = MolecularActivityId(self.molecular_activity) - - if self.target is not None and not isinstance(self.target, MoleculeId): - self.target = MoleculeId(self.target) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneSubcellularLocalizationRelationship(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneSubcellularLocalizationRelationship - class_class_curie: ClassVar[str] = "gocam:GeneSubcellularLocalizationRelationship" - class_name: ClassVar[str] = "GeneSubcellularLocalizationRelationship" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneSubcellularLocalizationRelationship - - gene: Optional[Union[str, GeneId]] = None - location: Optional[Union[str, GeneLocationId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.location is not None and not isinstance(self.location, GeneLocationId): - self.location = GeneLocationId(self.location) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneGeneInteraction(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = GOCAM.GeneGeneInteraction - class_class_curie: ClassVar[str] = "gocam:GeneGeneInteraction" - class_name: ClassVar[str] = "GeneGeneInteraction" - class_model_uri: ClassVar[URIRef] = GOCAM.GeneGeneInteraction - - gene1: Optional[Union[str, GeneId]] = None - gene2: Optional[Union[str, GeneId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene1 is not None and not isinstance(self.gene1, GeneId): - self.gene1 = GeneId(self.gene1) - - if self.gene2 is not None and not isinstance(self.gene2, GeneId): - self.gene2 = GeneId(self.gene2) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = GOCAM.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = GOCAM.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = GOCAM.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = GOCAM.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = GOCAM.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class GeneLocationEnum(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="GeneLocationEnum", - ) - -class GOCellComponentType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="GOCellComponentType", - ) - -class CellType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="CellType", - ) - -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.iBDAnnotations__genes = Slot(uri=GOCAM.genes, name="iBDAnnotations__genes", curie=GOCAM.curie('genes'), - model_uri=GOCAM.iBDAnnotations__genes, domain=None, range=Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]]) - -slots.iBDAnnotations__organisms = Slot(uri=GOCAM.organisms, name="iBDAnnotations__organisms", curie=GOCAM.curie('organisms'), - model_uri=GOCAM.iBDAnnotations__organisms, domain=None, range=Optional[Union[Union[str, OrganismId], List[Union[str, OrganismId]]]]) - -slots.iBDAnnotations__gene_organisms = Slot(uri=GOCAM.gene_organisms, name="iBDAnnotations__gene_organisms", curie=GOCAM.curie('gene_organisms'), - model_uri=GOCAM.iBDAnnotations__gene_organisms, domain=None, range=Optional[Union[Union[dict, GeneOrganismRelationship], List[Union[dict, GeneOrganismRelationship]]]]) - -slots.iBDAnnotations__activities = Slot(uri=GOCAM.activities, name="iBDAnnotations__activities", curie=GOCAM.curie('activities'), - model_uri=GOCAM.iBDAnnotations__activities, domain=None, range=Optional[Union[Union[str, MolecularActivityId], List[Union[str, MolecularActivityId]]]]) - -slots.iBDAnnotations__gene_functions = Slot(uri=GOCAM.gene_functions, name="iBDAnnotations__gene_functions", curie=GOCAM.curie('gene_functions'), - model_uri=GOCAM.iBDAnnotations__gene_functions, domain=None, range=Optional[Union[Union[dict, GeneMolecularActivityRelationship], List[Union[dict, GeneMolecularActivityRelationship]]]]) - -slots.iBDAnnotations__cellular_processes = Slot(uri=GOCAM.cellular_processes, name="iBDAnnotations__cellular_processes", curie=GOCAM.curie('cellular_processes'), - model_uri=GOCAM.iBDAnnotations__cellular_processes, domain=None, range=Optional[Union[Union[str, CellularProcessId], List[Union[str, CellularProcessId]]]]) - -slots.iBDAnnotations__pathways = Slot(uri=GOCAM.pathways, name="iBDAnnotations__pathways", curie=GOCAM.curie('pathways'), - model_uri=GOCAM.iBDAnnotations__pathways, domain=None, range=Optional[Union[Union[str, PathwayId], List[Union[str, PathwayId]]]]) - -slots.iBDAnnotations__gene_gene_interactions = Slot(uri=GOCAM.gene_gene_interactions, name="iBDAnnotations__gene_gene_interactions", curie=GOCAM.curie('gene_gene_interactions'), - model_uri=GOCAM.iBDAnnotations__gene_gene_interactions, domain=None, range=Optional[Union[Union[dict, GeneGeneInteraction], List[Union[dict, GeneGeneInteraction]]]]) - -slots.iBDAnnotations__gene_localizations = Slot(uri=GOCAM.gene_localizations, name="iBDAnnotations__gene_localizations", curie=GOCAM.curie('gene_localizations'), - model_uri=GOCAM.iBDAnnotations__gene_localizations, domain=None, range=Optional[Union[Union[dict, GeneSubcellularLocalizationRelationship], List[Union[dict, GeneSubcellularLocalizationRelationship]]]]) - -slots.geneOrganismRelationship__gene = Slot(uri=GOCAM.gene, name="geneOrganismRelationship__gene", curie=GOCAM.curie('gene'), - model_uri=GOCAM.geneOrganismRelationship__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneOrganismRelationship__organism = Slot(uri=GOCAM.organism, name="geneOrganismRelationship__organism", curie=GOCAM.curie('organism'), - model_uri=GOCAM.geneOrganismRelationship__organism, domain=None, range=Optional[Union[str, OrganismId]]) - -slots.geneMolecularActivityRelationship__gene = Slot(uri=GOCAM.gene, name="geneMolecularActivityRelationship__gene", curie=GOCAM.curie('gene'), - model_uri=GOCAM.geneMolecularActivityRelationship__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneMolecularActivityRelationship__molecular_activity = Slot(uri=GOCAM.molecular_activity, name="geneMolecularActivityRelationship__molecular_activity", curie=GOCAM.curie('molecular_activity'), - model_uri=GOCAM.geneMolecularActivityRelationship__molecular_activity, domain=None, range=Optional[Union[str, MolecularActivityId]]) - -slots.geneMolecularActivityRelationship2__gene = Slot(uri=GOCAM.gene, name="geneMolecularActivityRelationship2__gene", curie=GOCAM.curie('gene'), - model_uri=GOCAM.geneMolecularActivityRelationship2__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneMolecularActivityRelationship2__molecular_activity = Slot(uri=GOCAM.molecular_activity, name="geneMolecularActivityRelationship2__molecular_activity", curie=GOCAM.curie('molecular_activity'), - model_uri=GOCAM.geneMolecularActivityRelationship2__molecular_activity, domain=None, range=Optional[Union[str, MolecularActivityId]]) - -slots.geneMolecularActivityRelationship2__target = Slot(uri=GOCAM.target, name="geneMolecularActivityRelationship2__target", curie=GOCAM.curie('target'), - model_uri=GOCAM.geneMolecularActivityRelationship2__target, domain=None, range=Optional[Union[str, MoleculeId]]) - -slots.geneSubcellularLocalizationRelationship__gene = Slot(uri=GOCAM.gene, name="geneSubcellularLocalizationRelationship__gene", curie=GOCAM.curie('gene'), - model_uri=GOCAM.geneSubcellularLocalizationRelationship__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneSubcellularLocalizationRelationship__location = Slot(uri=GOCAM.location, name="geneSubcellularLocalizationRelationship__location", curie=GOCAM.curie('location'), - model_uri=GOCAM.geneSubcellularLocalizationRelationship__location, domain=None, range=Optional[Union[str, GeneLocationId]]) - -slots.geneGeneInteraction__gene1 = Slot(uri=GOCAM.gene1, name="geneGeneInteraction__gene1", curie=GOCAM.curie('gene1'), - model_uri=GOCAM.geneGeneInteraction__gene1, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneGeneInteraction__gene2 = Slot(uri=GOCAM.gene2, name="geneGeneInteraction__gene2", curie=GOCAM.curie('gene2'), - model_uri=GOCAM.geneGeneInteraction__gene2, domain=None, range=Optional[Union[str, GeneId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=GOCAM.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=GOCAM.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=GOCAM.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=GOCAM.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=GOCAM.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=GOCAM.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=GOCAM.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=GOCAM.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=GOCAM.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=GOCAM.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=GOCAM.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=GOCAM.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=GOCAM.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=GOCAM.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=GOCAM.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=GOCAM.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=GOCAM.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=GOCAM.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=GOCAM.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=GOCAM.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=GOCAM.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=GOCAM.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=GOCAM.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=GOCAM.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=GOCAM.annotatorResult__object_text, domain=None, range=Optional[str]) - -slots.GeneLocation_id = Slot(uri=GOCAM.id, name="GeneLocation_id", curie=GOCAM.curie('id'), - model_uri=GOCAM.GeneLocation_id, domain=GeneLocation, range=Union[str, GeneLocationId]) \ No newline at end of file diff --git a/projects/ibd/jsonld/ibd.context.jsonld b/projects/ibd/jsonld/ibd.context.jsonld deleted file mode 100644 index 32eb76735..000000000 --- a/projects/ibd/jsonld/ibd.context.jsonld +++ /dev/null @@ -1,191 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:54:05", - "source": "ibd.yaml" - }, - "@context": { - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "CL": { - "@id": "http://purl.obolibrary.org/obo/CL_", - "@prefix": true - }, - "EFO": "http://example.org/UNKNOWN/EFO/", - "GO": { - "@id": "http://purl.obolibrary.org/obo/GO_", - "@prefix": true - }, - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "NCBITaxon": "http://example.org/UNKNOWN/NCBITaxon/", - "PR": "http://example.org/UNKNOWN/PR/", - "PW": "http://example.org/UNKNOWN/PW/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "UBERON": "http://example.org/UNKNOWN/UBERON/", - "UniProtKB": "http://example.org/UNKNOWN/UniProtKB/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "gocam": "http://w3id.org/ontogpt/gocam/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/gocam/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "gene1": { - "@type": "@id" - }, - "gene2": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "gene": { - "@type": "@id" - }, - "molecular_activity": { - "@type": "@id" - }, - "target": { - "@type": "@id" - }, - "organism": { - "@type": "@id" - }, - "location": { - "@type": "@id" - }, - "activities": { - "@type": "@id" - }, - "cellular_processes": { - "@type": "@id" - }, - "gene_functions": { - "@type": "@id" - }, - "gene_gene_interactions": { - "@type": "@id" - }, - "gene_localizations": { - "@type": "@id" - }, - "gene_organisms": { - "@type": "@id" - }, - "genes": { - "@type": "@id" - }, - "organisms": { - "@type": "@id" - }, - "pathways": { - "@type": "@id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/ibd/jsonld/ibd.jsonld b/projects/ibd/jsonld/ibd.jsonld deleted file mode 100644 index 374f60cd9..000000000 --- a/projects/ibd/jsonld/ibd.jsonld +++ /dev/null @@ -1,1767 +0,0 @@ -{ - "name": "gocam-template", - "description": "A template for GO-CAMs", - "title": "GO-CAM Template", - "id": "http://w3id.org/ontogpt/gocam", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "gocam", - "prefix_reference": "http://w3id.org/ontogpt/gocam/" - }, - { - "prefix_prefix": "GO", - "prefix_reference": "http://purl.obolibrary.org/obo/GO_" - }, - { - "prefix_prefix": "CL", - "prefix_reference": "http://purl.obolibrary.org/obo/CL_" - } - ], - "default_prefix": "gocam", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "GeneLocationEnum", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneLocationEnum", - "from_schema": "http://w3id.org/ontogpt/gocam", - "inherits": [ - "GOCellComponent", - "CellType" - ] - }, - { - "name": "GOCellComponentType", - "definition_uri": "http://w3id.org/ontogpt/gocam/GOCellComponentType", - "from_schema": "http://w3id.org/ontogpt/gocam", - "reachable_from": { - "source_ontology": "obo:go", - "source_nodes": [ - "GO:0005575" - ] - } - }, - { - "name": "CellType", - "definition_uri": "http://w3id.org/ontogpt/gocam/CellType", - "from_schema": "http://w3id.org/ontogpt/gocam", - "reachable_from": { - "source_ontology": "obo:cl", - "source_nodes": [ - "CL:0000000" - ] - } - }, - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "iBDAnnotations__genes", - "description": "semicolon-separated list of genes", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/genes", - "multivalued": true, - "alias": "genes", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__organisms", - "description": "semicolon-separated list of organism taxons", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/organisms", - "multivalued": true, - "alias": "organisms", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__gene_organisms", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of asterisk separated gene to organism relationships", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene_organisms", - "multivalued": true, - "alias": "gene_organisms", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "GeneOrganismRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__activities", - "description": "semicolon-separated list of molecular activities", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/activities", - "multivalued": true, - "alias": "activities", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__gene_functions", - "description": "semicolon-separated list of gene to molecular activity relationships", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene_functions", - "multivalued": true, - "alias": "gene_functions", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "GeneMolecularActivityRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__cellular_processes", - "description": "semicolon-separated list of cellular processes", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/cellular_processes", - "multivalued": true, - "alias": "cellular_processes", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "CellularProcess", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__pathways", - "description": "semicolon-separated list of pathways", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/pathways", - "multivalued": true, - "alias": "pathways", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "Pathway", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__gene_gene_interactions", - "description": "semicolon-separated list of gene to gene interactions", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene_gene_interactions", - "multivalued": true, - "alias": "gene_gene_interactions", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "GeneGeneInteraction", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__gene_localizations", - "description": "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene_localizations", - "multivalued": true, - "alias": "gene_localizations", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "GeneSubcellularLocalizationRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "geneOrganismRelationship__gene", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene", - "alias": "gene", - "owner": "GeneOrganismRelationship", - "domain_of": [ - "GeneOrganismRelationship" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneOrganismRelationship__organism", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/organism", - "alias": "organism", - "owner": "GeneOrganismRelationship", - "domain_of": [ - "GeneOrganismRelationship" - ], - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship__gene", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the gene in the pair. This comes first.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene", - "alias": "gene", - "owner": "GeneMolecularActivityRelationship", - "domain_of": [ - "GeneMolecularActivityRelationship" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship__molecular_activity", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular function in the pair. This comes second. May be a GO term.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/molecular_activity", - "alias": "molecular_activity", - "owner": "GeneMolecularActivityRelationship", - "domain_of": [ - "GeneMolecularActivityRelationship" - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship2__gene", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the gene.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene", - "alias": "gene", - "owner": "GeneMolecularActivityRelationship2", - "domain_of": [ - "GeneMolecularActivityRelationship2" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship2__molecular_activity", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular activity, for example, ubiquitination. May be a GO term.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/molecular_activity", - "alias": "molecular_activity", - "owner": "GeneMolecularActivityRelationship2", - "domain_of": [ - "GeneMolecularActivityRelationship2" - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "geneMolecularActivityRelationship2__target", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular entity that is the target of the molecular activity.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/target", - "alias": "target", - "owner": "GeneMolecularActivityRelationship2", - "domain_of": [ - "GeneMolecularActivityRelationship2" - ], - "range": "Molecule", - "@type": "SlotDefinition" - }, - { - "name": "geneSubcellularLocalizationRelationship__gene", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene", - "alias": "gene", - "owner": "GeneSubcellularLocalizationRelationship", - "domain_of": [ - "GeneSubcellularLocalizationRelationship" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneSubcellularLocalizationRelationship__location", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/location", - "alias": "location", - "owner": "GeneSubcellularLocalizationRelationship", - "domain_of": [ - "GeneSubcellularLocalizationRelationship" - ], - "range": "GeneLocation", - "@type": "SlotDefinition" - }, - { - "name": "geneGeneInteraction__gene1", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene1", - "alias": "gene1", - "owner": "GeneGeneInteraction", - "domain_of": [ - "GeneGeneInteraction" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneGeneInteraction__gene2", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slot_uri": "http://w3id.org/ontogpt/gocam/gene2", - "alias": "gene2", - "owner": "GeneGeneInteraction", - "domain_of": [ - "GeneGeneInteraction" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "GeneLocation_id", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "namedEntity__id", - "values_from": [ - "GOCellComponentType", - "CellType" - ], - "domain": "GeneLocation", - "slot_uri": "http://w3id.org/ontogpt/gocam/id", - "identifier": true, - "alias": "id", - "owner": "GeneLocation", - "domain_of": [ - "GeneLocation" - ], - "is_usage_slot": true, - "usage_slot_name": "id", - "range": "string", - "required": true, - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "IBDAnnotations", - "definition_uri": "http://w3id.org/ontogpt/gocam/IBDAnnotations", - "from_schema": "http://w3id.org/ontogpt/gocam", - "slots": [ - "iBDAnnotations__genes", - "iBDAnnotations__organisms", - "iBDAnnotations__gene_organisms", - "iBDAnnotations__activities", - "iBDAnnotations__gene_functions", - "iBDAnnotations__cellular_processes", - "iBDAnnotations__pathways", - "iBDAnnotations__gene_gene_interactions", - "iBDAnnotations__gene_localizations" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "genes", - "description": "semicolon-separated list of genes", - "multivalued": true, - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "organisms", - "description": "semicolon-separated list of organism taxons", - "multivalued": true, - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "gene_organisms", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of asterisk separated gene to organism relationships", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "GeneOrganismRelationship", - "@type": "SlotDefinition" - }, - { - "name": "activities", - "description": "semicolon-separated list of molecular activities", - "multivalued": true, - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "gene_functions", - "description": "semicolon-separated list of gene to molecular activity relationships", - "multivalued": true, - "range": "GeneMolecularActivityRelationship", - "@type": "SlotDefinition" - }, - { - "name": "cellular_processes", - "description": "semicolon-separated list of cellular processes", - "multivalued": true, - "range": "CellularProcess", - "@type": "SlotDefinition" - }, - { - "name": "pathways", - "description": "semicolon-separated list of pathways", - "multivalued": true, - "range": "Pathway", - "@type": "SlotDefinition" - }, - { - "name": "gene_gene_interactions", - "description": "semicolon-separated list of gene to gene interactions", - "multivalued": true, - "range": "GeneGeneInteraction", - "@type": "SlotDefinition" - }, - { - "name": "gene_localizations", - "description": "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"", - "multivalued": true, - "range": "GeneSubcellularLocalizationRelationship", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/IBDAnnotations", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Gene", - "id_prefixes": [ - "HGNC", - "PR", - "UniProtKB" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/Gene", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, bioportal:hgnc-nr", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/Gene", - "@type": "ClassDefinition" - }, - { - "name": "Pathway", - "id_prefixes": [ - "GO", - "PW" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/Pathway", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go, sqlite:obo:pw", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/Pathway", - "@type": "ClassDefinition" - }, - { - "name": "CellularProcess", - "id_prefixes": [ - "GO" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/CellularProcess", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/CellularProcess", - "@type": "ClassDefinition" - }, - { - "name": "MolecularActivity", - "id_prefixes": [ - "GO" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/MolecularActivity", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/MolecularActivity", - "@type": "ClassDefinition" - }, - { - "name": "GeneLocation", - "id_prefixes": [ - "GO", - "CL", - "UBERON" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneLocation", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go, sqlite:obo:cl", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__label", - "GeneLocation_id" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/GeneLocation", - "@type": "ClassDefinition" - }, - { - "name": "Organism", - "id_prefixes": [ - "NCBITaxon", - "EFO" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/Organism", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, sqlite:obo:ncbitaxon", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/Organism", - "@type": "ClassDefinition" - }, - { - "name": "Molecule", - "id_prefixes": [ - "CHEBI", - "PR" - ], - "definition_uri": "http://w3id.org/ontogpt/gocam/Molecule", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, sqlite:obo:chebi", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/gocam/Molecule", - "@type": "ClassDefinition" - }, - { - "name": "GeneOrganismRelationship", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneOrganismRelationship", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneOrganismRelationship__gene", - "geneOrganismRelationship__organism" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "organism", - "range": "Organism", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneOrganismRelationship", - "@type": "ClassDefinition" - }, - { - "name": "GeneMolecularActivityRelationship", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship", - "annotations": [ - { - "tag": "prompt.example", - "value": "TODO\n\ngene: HGNC:1234\nmolecular_activity: GO:0003674", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneMolecularActivityRelationship__gene", - "geneMolecularActivityRelationship__molecular_activity" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the gene in the pair. This comes first.", - "@type": "Annotation" - } - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "molecular_activity", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular function in the pair. This comes second. May be a GO term.", - "@type": "Annotation" - } - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship", - "@type": "ClassDefinition" - }, - { - "name": "GeneMolecularActivityRelationship2", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship2", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneMolecularActivityRelationship2__gene", - "geneMolecularActivityRelationship2__molecular_activity", - "geneMolecularActivityRelationship2__target" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the gene.", - "@type": "Annotation" - } - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "molecular_activity", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular activity, for example, ubiquitination. May be a GO term.", - "@type": "Annotation" - } - ], - "range": "MolecularActivity", - "@type": "SlotDefinition" - }, - { - "name": "target", - "annotations": [ - { - "tag": "prompt", - "value": "the name of the molecular entity that is the target of the molecular activity.", - "@type": "Annotation" - } - ], - "range": "Molecule", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship2", - "@type": "ClassDefinition" - }, - { - "name": "GeneSubcellularLocalizationRelationship", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneSubcellularLocalizationRelationship", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneSubcellularLocalizationRelationship__gene", - "geneSubcellularLocalizationRelationship__location" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "location", - "range": "GeneLocation", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneSubcellularLocalizationRelationship", - "@type": "ClassDefinition" - }, - { - "name": "GeneGeneInteraction", - "definition_uri": "http://w3id.org/ontogpt/gocam/GeneGeneInteraction", - "from_schema": "http://w3id.org/ontogpt/gocam", - "is_a": "CompoundExpression", - "slots": [ - "geneGeneInteraction__gene1", - "geneGeneInteraction__gene2" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene1", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "gene2", - "range": "Gene", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/gocam/GeneGeneInteraction", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "ibd.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 4869, - "generation_date": "2023-08-07T10:54:06", - "@type": "SchemaDefinition", - "@context": [ - "projects/ibd/jsonld/ibd.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/gocam/" - } - ] -} diff --git a/projects/ibd/jsonschema/ibd.schema.json b/projects/ibd/jsonschema/ibd.schema.json deleted file mode 100644 index 8d813645b..000000000 --- a/projects/ibd/jsonschema/ibd.schema.json +++ /dev/null @@ -1,499 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "CellType": { - "description": "", - "enum": [], - "title": "CellType", - "type": "string" - }, - "CellularProcess": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "CellularProcess", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "GOCellComponentType": { - "description": "", - "enum": [], - "title": "GOCellComponentType", - "type": "string" - }, - "Gene": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Gene", - "type": "object" - }, - "GeneGeneInteraction": { - "additionalProperties": false, - "description": "", - "properties": { - "gene1": { - "type": "string" - }, - "gene2": { - "type": "string" - } - }, - "title": "GeneGeneInteraction", - "type": "object" - }, - "GeneLocation": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "GeneLocation", - "type": "object" - }, - "GeneLocationEnum": { - "description": "", - "enum": [], - "title": "GeneLocationEnum", - "type": "string" - }, - "GeneMolecularActivityRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "type": "string" - }, - "molecular_activity": { - "type": "string" - } - }, - "title": "GeneMolecularActivityRelationship", - "type": "object" - }, - "GeneMolecularActivityRelationship2": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "type": "string" - }, - "molecular_activity": { - "type": "string" - }, - "target": { - "type": "string" - } - }, - "title": "GeneMolecularActivityRelationship2", - "type": "object" - }, - "GeneOrganismRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "type": "string" - }, - "organism": { - "type": "string" - } - }, - "title": "GeneOrganismRelationship", - "type": "object" - }, - "GeneSubcellularLocalizationRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "type": "string" - }, - "location": { - "type": "string" - } - }, - "title": "GeneSubcellularLocalizationRelationship", - "type": "object" - }, - "IBDAnnotations": { - "additionalProperties": false, - "description": "", - "properties": { - "activities": { - "description": "semicolon-separated list of molecular activities", - "items": { - "type": "string" - }, - "type": "array" - }, - "cellular_processes": { - "description": "semicolon-separated list of cellular processes", - "items": { - "type": "string" - }, - "type": "array" - }, - "gene_functions": { - "description": "semicolon-separated list of gene to molecular activity relationships", - "items": { - "$ref": "#/$defs/GeneMolecularActivityRelationship" - }, - "type": "array" - }, - "gene_gene_interactions": { - "description": "semicolon-separated list of gene to gene interactions", - "items": { - "$ref": "#/$defs/GeneGeneInteraction" - }, - "type": "array" - }, - "gene_localizations": { - "description": "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"", - "items": { - "$ref": "#/$defs/GeneSubcellularLocalizationRelationship" - }, - "type": "array" - }, - "gene_organisms": { - "items": { - "$ref": "#/$defs/GeneOrganismRelationship" - }, - "type": "array" - }, - "genes": { - "description": "semicolon-separated list of genes", - "items": { - "type": "string" - }, - "type": "array" - }, - "organisms": { - "description": "semicolon-separated list of organism taxons", - "items": { - "type": "string" - }, - "type": "array" - }, - "pathways": { - "description": "semicolon-separated list of pathways", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "IBDAnnotations", - "type": "object" - }, - "MolecularActivity": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "MolecularActivity", - "type": "object" - }, - "Molecule": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Molecule", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Organism": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Organism", - "type": "object" - }, - "Pathway": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Pathway", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/gocam", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "activities": { - "description": "semicolon-separated list of molecular activities", - "items": { - "type": "string" - }, - "type": "array" - }, - "cellular_processes": { - "description": "semicolon-separated list of cellular processes", - "items": { - "type": "string" - }, - "type": "array" - }, - "gene_functions": { - "description": "semicolon-separated list of gene to molecular activity relationships", - "items": { - "$ref": "#/$defs/GeneMolecularActivityRelationship" - }, - "type": "array" - }, - "gene_gene_interactions": { - "description": "semicolon-separated list of gene to gene interactions", - "items": { - "$ref": "#/$defs/GeneGeneInteraction" - }, - "type": "array" - }, - "gene_localizations": { - "description": "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"", - "items": { - "$ref": "#/$defs/GeneSubcellularLocalizationRelationship" - }, - "type": "array" - }, - "gene_organisms": { - "items": { - "$ref": "#/$defs/GeneOrganismRelationship" - }, - "type": "array" - }, - "genes": { - "description": "semicolon-separated list of genes", - "items": { - "type": "string" - }, - "type": "array" - }, - "organisms": { - "description": "semicolon-separated list of organism taxons", - "items": { - "type": "string" - }, - "type": "array" - }, - "pathways": { - "description": "semicolon-separated list of pathways", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "gocam-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/ibd/owl/ibd.owl.ttl b/projects/ibd/owl/ibd.owl.ttl deleted file mode 100644 index 254cfbce4..000000000 --- a/projects/ibd/owl/ibd.owl.ttl +++ /dev/null @@ -1,638 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix gocam: <http://w3id.org/ontogpt/gocam/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/gocam> a owl:Ontology ; - rdfs:label "gocam-template" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - gocam:IBDAnnotations ; - linkml:classes "{'IBDAnnotations': ClassDefinition(name='IBDAnnotations', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/IBDAnnotations', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iBDAnnotations__genes', 'iBDAnnotations__organisms', 'iBDAnnotations__gene_organisms', 'iBDAnnotations__activities', 'iBDAnnotations__gene_functions', 'iBDAnnotations__cellular_processes', 'iBDAnnotations__pathways', 'iBDAnnotations__gene_gene_interactions', 'iBDAnnotations__gene_localizations'], slot_usage={}, attributes={'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organisms': SlotDefinition(name='organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of organism taxons', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_organisms': SlotDefinition(name='gene_organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of asterisk separated gene to organism relationships', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneOrganismRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'activities': SlotDefinition(name='activities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of molecular activities', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_functions': SlotDefinition(name='gene_functions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to molecular activity relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneMolecularActivityRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'cellular_processes': SlotDefinition(name='cellular_processes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of cellular processes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CellularProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'pathways': SlotDefinition(name='pathways', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of pathways', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Pathway', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_gene_interactions': SlotDefinition(name='gene_gene_interactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to gene interactions', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneGeneInteraction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_localizations': SlotDefinition(name='gene_localizations', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneSubcellularLocalizationRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:IBDAnnotations', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC', 'PR', 'UniProtKB'], definition_uri='http://w3id.org/ontogpt/gocam/Gene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, bioportal:hgnc-nr', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Pathway': ClassDefinition(name='Pathway', id_prefixes=['GO', 'PW'], definition_uri='http://w3id.org/ontogpt/gocam/Pathway', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:pw', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:Pathway', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CellularProcess': ClassDefinition(name='CellularProcess', id_prefixes=['GO'], definition_uri='http://w3id.org/ontogpt/gocam/CellularProcess', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:CellularProcess', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'MolecularActivity': ClassDefinition(name='MolecularActivity', id_prefixes=['GO'], definition_uri='http://w3id.org/ontogpt/gocam/MolecularActivity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:MolecularActivity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneLocation': ClassDefinition(name='GeneLocation', id_prefixes=['GO', 'CL', 'UBERON'], definition_uri='http://w3id.org/ontogpt/gocam/GeneLocation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:cl', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__label', 'GeneLocation_id'], slot_usage={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='namedEntity__id', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['GOCellComponentType', 'CellType'], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='gocam:GeneLocation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Organism': ClassDefinition(name='Organism', id_prefixes=['NCBITaxon', 'EFO'], definition_uri='http://w3id.org/ontogpt/gocam/Organism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, sqlite:obo:ncbitaxon', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:Organism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Molecule': ClassDefinition(name='Molecule', id_prefixes=['CHEBI', 'PR'], definition_uri='http://w3id.org/ontogpt/gocam/Molecule', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, sqlite:obo:chebi', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='gocam:Molecule', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneOrganismRelationship': ClassDefinition(name='GeneOrganismRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneOrganismRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneOrganismRelationship__gene', 'geneOrganismRelationship__organism'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organism': SlotDefinition(name='organism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneOrganismRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneMolecularActivityRelationship': ClassDefinition(name='GeneMolecularActivityRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.example': Annotation(tag='prompt.example', value='TODO\\n\\ngene: HGNC:1234\\nmolecular_activity: GO:0003674', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneMolecularActivityRelationship__gene', 'geneMolecularActivityRelationship__molecular_activity'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the gene in the pair. This comes first.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular function in the pair. This comes second. May be a GO term.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneMolecularActivityRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneMolecularActivityRelationship2': ClassDefinition(name='GeneMolecularActivityRelationship2', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneMolecularActivityRelationship2', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneMolecularActivityRelationship2__gene', 'geneMolecularActivityRelationship2__molecular_activity', 'geneMolecularActivityRelationship2__target'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the gene.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular activity, for example, ubiquitination. May be a GO term.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'target': SlotDefinition(name='target', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular entity that is the target of the molecular activity.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Molecule', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneMolecularActivityRelationship2', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneSubcellularLocalizationRelationship': ClassDefinition(name='GeneSubcellularLocalizationRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneSubcellularLocalizationRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneSubcellularLocalizationRelationship__gene', 'geneSubcellularLocalizationRelationship__location'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneLocation', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneSubcellularLocalizationRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneGeneInteraction': ClassDefinition(name='GeneGeneInteraction', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneGeneInteraction', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneGeneInteraction__gene1', 'geneGeneInteraction__gene2'], slot_usage={}, attributes={'gene1': SlotDefinition(name='gene1', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene2': SlotDefinition(name='gene2', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='gocam:GeneGeneInteraction', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'GeneLocationEnum': EnumDefinition(name='GeneLocationEnum', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GeneLocationEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=['GOCellComponent', 'CellType'], reachable_from=None, matches=None, concepts=[]), 'GOCellComponentType': EnumDefinition(name='GOCellComponentType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/GOCellComponentType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:go', source_nodes=['GO:0005575'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'CellType': EnumDefinition(name='CellType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/gocam/CellType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/gocam', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:cl', source_nodes=['CL:0000000'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/gocam" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -gocam:CellType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "CellType" ; - owl:unionOf [ rdf:rest () ] . - -gocam:GOCellComponentType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "GOCellComponentType" ; - owl:unionOf [ rdf:rest () ] . - -gocam:GeneLocationEnum a owl:Class, - linkml:EnumDefinition ; - rdfs:label "GeneLocationEnum" ; - owl:unionOf [ rdf:rest () ] . - -gocam:GeneMolecularActivityRelationship2 a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneMolecularActivityRelationship2" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:MolecularActivity ; - owl:onProperty gocam:molecular_activity ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Molecule ; - owl:onProperty gocam:target ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the gene.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular activity, for example, ubiquitination. May be a GO term.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'target': SlotDefinition(name='target', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular entity that is the target of the molecular activity.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Molecule', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - gocam:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -gocam:IBDAnnotations a owl:Class, - linkml:ClassDefinition ; - rdfs:label "IBDAnnotations" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom gocam:MolecularActivity ; - owl:onProperty gocam:activities ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:GeneOrganismRelationship ; - owl:onProperty gocam:gene_organisms ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:GeneGeneInteraction ; - owl:onProperty gocam:gene_gene_interactions ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:Pathway ; - owl:onProperty gocam:pathways ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:GeneMolecularActivityRelationship ; - owl:onProperty gocam:gene_functions ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:Gene ; - owl:onProperty gocam:genes ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:Organism ; - owl:onProperty gocam:organisms ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:CellularProcess ; - owl:onProperty gocam:cellular_processes ], - [ a owl:Restriction ; - owl:allValuesFrom gocam:GeneSubcellularLocalizationRelationship ; - owl:onProperty gocam:gene_localizations ] ; - linkml:attributes "{'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organisms': SlotDefinition(name='organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of organism taxons', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_organisms': SlotDefinition(name='gene_organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of asterisk separated gene to organism relationships', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneOrganismRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'activities': SlotDefinition(name='activities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of molecular activities', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_functions': SlotDefinition(name='gene_functions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to molecular activity relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneMolecularActivityRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'cellular_processes': SlotDefinition(name='cellular_processes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of cellular processes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CellularProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'pathways': SlotDefinition(name='pathways', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of pathways', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Pathway', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_gene_interactions': SlotDefinition(name='gene_gene_interactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to gene interactions', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneGeneInteraction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_localizations': SlotDefinition(name='gene_localizations', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneSubcellularLocalizationRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -gocam:activities a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "activities" ; - rdfs:range gocam:MolecularActivity ; - skos:definition "semicolon-separated list of molecular activities" . - -gocam:cellular_processes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "cellular_processes" ; - rdfs:range gocam:CellularProcess ; - skos:definition "semicolon-separated list of cellular processes" . - -gocam:gene1 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene1" ; - rdfs:range gocam:Gene . - -gocam:gene2 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene2" ; - rdfs:range gocam:Gene . - -gocam:gene_functions a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_functions" ; - rdfs:range gocam:GeneMolecularActivityRelationship ; - skos:definition "semicolon-separated list of gene to molecular activity relationships" . - -gocam:gene_gene_interactions a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_gene_interactions" ; - rdfs:range gocam:GeneGeneInteraction ; - skos:definition "semicolon-separated list of gene to gene interactions" . - -gocam:gene_localizations a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_localizations" ; - rdfs:range gocam:GeneSubcellularLocalizationRelationship ; - skos:definition "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"" . - -gocam:gene_organisms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_organisms" ; - gocam:prompt "semicolon-separated list of asterisk separated gene to organism relationships" ; - rdfs:range gocam:GeneOrganismRelationship . - -gocam:genes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "genes" ; - rdfs:range gocam:Gene ; - skos:definition "semicolon-separated list of genes" . - -gocam:id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "id" ; - rdfs:domain gocam:GeneLocation ; - rdfs:range linkml:String ; - rdfs:subPropertyOf <http://w3id.org/ontogpt/core/id> ; - linkml:is_a "namedEntity__id" . - -gocam:location a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "location" ; - rdfs:range gocam:GeneLocation . - -gocam:organism a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "organism" ; - rdfs:range gocam:Organism . - -gocam:organisms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "organisms" ; - rdfs:range gocam:Organism ; - skos:definition "semicolon-separated list of organism taxons" . - -gocam:pathways a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "pathways" ; - rdfs:range gocam:Pathway ; - skos:definition "semicolon-separated list of pathways" . - -gocam:target a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "target" ; - gocam:prompt "the name of the molecular entity that is the target of the molecular activity." ; - rdfs:range gocam:Molecule . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - gocam:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:CellularProcess a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CellularProcess" ; - gocam:annotators "sqlite:obo:go" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:GeneGeneInteraction a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneGeneInteraction" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene2 ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene1': SlotDefinition(name='gene1', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene2': SlotDefinition(name='gene2', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:GeneMolecularActivityRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneMolecularActivityRelationship" ; - gocam:prompt.example """TODO - -gene: HGNC:1234 -molecular_activity: GO:0003674""" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:MolecularActivity ; - owl:onProperty gocam:molecular_activity ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the gene in the pair. This comes first.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'molecular_activity': SlotDefinition(name='molecular_activity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='the name of the molecular function in the pair. This comes second. May be a GO term.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MolecularActivity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:GeneOrganismRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneOrganismRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Organism ; - owl:onProperty gocam:organism ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organism': SlotDefinition(name='organism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:GeneSubcellularLocalizationRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneSubcellularLocalizationRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:GeneLocation ; - owl:onProperty gocam:location ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass gocam:Gene ; - owl:onProperty gocam:gene ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneLocation', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -gocam:Molecule a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Molecule" ; - gocam:annotators "gilda:, sqlite:obo:chebi" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:Pathway a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Pathway" ; - gocam:annotators "sqlite:obo:go, sqlite:obo:pw" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:molecular_activity a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -gocam:GeneLocation a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneLocation" ; - gocam:annotators "sqlite:obo:go, sqlite:obo:cl" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty gocam:id ; - owl:qualifiedCardinality 1 ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:MolecularActivity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MolecularActivity" ; - gocam:annotators "sqlite:obo:go" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:Organism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Organism" ; - gocam:annotators "gilda:, sqlite:obo:ncbitaxon" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -gocam:gene a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -gocam:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - gocam:annotators "gilda:, bioportal:hgnc-nr" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/ibd/prefixmap/ibd.yaml b/projects/ibd/prefixmap/ibd.yaml deleted file mode 100644 index e38e646ee..000000000 --- a/projects/ibd/prefixmap/ibd.yaml +++ /dev/null @@ -1,45 +0,0 @@ -{ - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "CL": "http://purl.obolibrary.org/obo/CL_", - "EFO": "http://example.org/UNKNOWN/EFO/", - "GO": "http://purl.obolibrary.org/obo/GO_", - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "NCBITaxon": "http://example.org/UNKNOWN/NCBITaxon/", - "PR": "http://example.org/UNKNOWN/PR/", - "PW": "http://example.org/UNKNOWN/PW/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "UBERON": "http://example.org/UNKNOWN/UBERON/", - "UniProtKB": "http://example.org/UNKNOWN/UniProtKB/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "gocam": "http://w3id.org/ontogpt/gocam/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/ibd/protobuf/ibd.proto b/projects/ibd/protobuf/ibd.proto deleted file mode 100644 index d4e73bcc6..000000000 --- a/projects/ibd/protobuf/ibd.proto +++ /dev/null @@ -1,108 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message CellularProcess - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -message GeneGeneInteraction - { - gene gene1 = 0 - gene gene2 = 0 - } -message GeneLocation - { - string label = 0 - string id = 0 - } -message GeneMolecularActivityRelationship - { - gene gene = 0 - molecularActivity molecularActivity = 0 - } -message GeneMolecularActivityRelationship2 - { - gene gene = 0 - molecularActivity molecularActivity = 0 - molecule target = 0 - } -message GeneOrganismRelationship - { - gene gene = 0 - organism organism = 0 - } -message GeneSubcellularLocalizationRelationship - { - gene gene = 0 - geneLocation location = 0 - } -message IBDAnnotations - { - repeated gene genes = 0 - repeated organism organisms = 0 - repeated geneOrganismRelationship geneOrganisms = 0 - repeated molecularActivity activities = 0 - repeated geneMolecularActivityRelationship geneFunctions = 0 - repeated cellularProcess cellularProcesses = 0 - repeated pathway pathways = 0 - repeated geneGeneInteraction geneGeneInteractions = 0 - repeated geneSubcellularLocalizationRelationship geneLocalizations = 0 - } -message MolecularActivity - { - string id = 0 - string label = 0 - } -message Molecule - { - string id = 0 - string label = 0 - } -message Organism - { - string id = 0 - string label = 0 - } -message Pathway - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/ibd/shacl/ibd.shacl.ttl b/projects/ibd/shacl/ibd.shacl.ttl deleted file mode 100644 index 623a2bd88..000000000 --- a/projects/ibd/shacl/ibd.shacl.ttl +++ /dev/null @@ -1,391 +0,0 @@ -@prefix gocam: <http://w3id.org/ontogpt/gocam/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -gocam:GeneMolecularActivityRelationship2 a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene ], - [ sh:class gocam:MolecularActivity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:molecular_activity ], - [ sh:class gocam:Molecule ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path gocam:target ] ; - sh:targetClass gocam:GeneMolecularActivityRelationship2 . - -gocam:IBDAnnotations a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:GeneSubcellularLocalizationRelationship ; - sh:description "semicolon-separated list of genes plus their location in the cell; for example, \"gene1 / cytoplasm; gene2 / mitochondrion\"" ; - sh:nodeKind sh:BlankNode ; - sh:order 8 ; - sh:path gocam:gene_localizations ], - [ sh:class gocam:Gene ; - sh:description "semicolon-separated list of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:genes ], - [ sh:class gocam:CellularProcess ; - sh:description "semicolon-separated list of cellular processes" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path gocam:cellular_processes ], - [ sh:class gocam:Organism ; - sh:description "semicolon-separated list of organism taxons" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:organisms ], - [ sh:class gocam:GeneGeneInteraction ; - sh:description "semicolon-separated list of gene to gene interactions" ; - sh:nodeKind sh:BlankNode ; - sh:order 7 ; - sh:path gocam:gene_gene_interactions ], - [ sh:class gocam:Pathway ; - sh:description "semicolon-separated list of pathways" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path gocam:pathways ], - [ sh:class gocam:GeneMolecularActivityRelationship ; - sh:description "semicolon-separated list of gene to molecular activity relationships" ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path gocam:gene_functions ], - [ sh:class gocam:MolecularActivity ; - sh:description "semicolon-separated list of molecular activities" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path gocam:activities ], - [ sh:class gocam:GeneOrganismRelationship ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path gocam:gene_organisms ] ; - sh:targetClass gocam:IBDAnnotations . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -gocam:CellularProcess a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:CellularProcess . - -gocam:GeneGeneInteraction a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene1 ], - [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:gene2 ] ; - sh:targetClass gocam:GeneGeneInteraction . - -gocam:GeneLocation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:GeneLocation . - -gocam:GeneMolecularActivityRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:MolecularActivity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:molecular_activity ], - [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene ] ; - sh:targetClass gocam:GeneMolecularActivityRelationship . - -gocam:GeneOrganismRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:Organism ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:organism ], - [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene ] ; - sh:targetClass gocam:GeneOrganismRelationship . - -gocam:GeneSubcellularLocalizationRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class gocam:Gene ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path gocam:gene ], - [ sh:class gocam:GeneLocation ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path gocam:location ] ; - sh:targetClass gocam:GeneSubcellularLocalizationRelationship . - -gocam:Molecule a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:Molecule . - -gocam:Pathway a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:Pathway . - -gocam:Organism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass gocam:Organism . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -gocam:MolecularActivity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:MolecularActivity . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - -gocam:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass gocam:Gene . - diff --git a/projects/ibd/shex/ibd.shex b/projects/ibd/shex/ibd.shex deleted file mode 100644 index 90266fb11..000000000 --- a/projects/ibd/shex/ibd.shex +++ /dev/null @@ -1,260 +0,0 @@ -BASE <http://w3id.org/ontogpt/gocam/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<CellularProcess> CLOSED { - ( $<CellularProcess_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <CellularProcess> ] - ) -} - -core:CompoundExpression ( - @<GeneGeneInteraction> OR @<GeneMolecularActivityRelationship> OR @<GeneMolecularActivityRelationship2> OR - @<GeneOrganismRelationship> OR @<GeneSubcellularLocalizationRelationship> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<Gene> CLOSED { - ( $<Gene_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Gene> ] - ) -} - -<GeneGeneInteraction> CLOSED { - ( $<GeneGeneInteraction_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene1> @<Gene> ? ; - <gene2> @<Gene> ? - ) ; - rdf:type [ <GeneGeneInteraction> ] ? - ) -} - -<GeneLocation> CLOSED { - ( $<GeneLocation_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <GeneLocation> ] - ) -} - -<GeneMolecularActivityRelationship> CLOSED { - ( $<GeneMolecularActivityRelationship_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <molecular_activity> @<MolecularActivity> ? - ) ; - rdf:type [ <GeneMolecularActivityRelationship> ] ? - ) -} - -<GeneMolecularActivityRelationship2> CLOSED { - ( $<GeneMolecularActivityRelationship2_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <molecular_activity> @<MolecularActivity> ? ; - <target> @<Molecule> ? - ) ; - rdf:type [ <GeneMolecularActivityRelationship2> ] ? - ) -} - -<GeneOrganismRelationship> CLOSED { - ( $<GeneOrganismRelationship_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <organism> @<Organism> ? - ) ; - rdf:type [ <GeneOrganismRelationship> ] ? - ) -} - -<GeneSubcellularLocalizationRelationship> CLOSED { - ( $<GeneSubcellularLocalizationRelationship_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <location> @<GeneLocation> ? - ) ; - rdf:type [ <GeneSubcellularLocalizationRelationship> ] ? - ) -} - -<IBDAnnotations> CLOSED { - ( $<IBDAnnotations_tes> ( <genes> @<Gene> * ; - <organisms> @<Organism> * ; - <gene_organisms> @<GeneOrganismRelationship> * ; - <activities> @<MolecularActivity> * ; - <gene_functions> @<GeneMolecularActivityRelationship> * ; - <cellular_processes> @<CellularProcess> * ; - <pathways> @<Pathway> * ; - <gene_gene_interactions> @<GeneGeneInteraction> * ; - <gene_localizations> @<GeneSubcellularLocalizationRelationship> * - ) ; - rdf:type [ <IBDAnnotations> ] ? - ) -} - -<MolecularActivity> CLOSED { - ( $<MolecularActivity_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <MolecularActivity> ] - ) -} - -<Molecule> CLOSED { - ( $<Molecule_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Molecule> ] - ) -} - -core:NamedEntity ( - @<CellularProcess> OR @<Gene> OR @<GeneLocation> OR @<MolecularActivity> OR @<Molecule> OR @<Organism> OR @<Pathway> OR - @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<Organism> CLOSED { - ( $<Organism_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Organism> ] - ) -} - -<Pathway> CLOSED { - ( $<Pathway_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Pathway> ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/ibd/sqlschema/ibd.sql b/projects/ibd/sqlschema/ibd.sql deleted file mode 100644 index 6bb0e0191..000000000 --- a/projects/ibd/sqlschema/ibd.sql +++ /dev/null @@ -1,137 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "CellularProcess" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "GeneLocation" ( - label TEXT, - id TEXT NOT NULL, - PRIMARY KEY (id) -); - -CREATE TABLE "IBDAnnotations" ( - genes TEXT, - organisms TEXT, - gene_organisms TEXT, - activities TEXT, - gene_functions TEXT, - cellular_processes TEXT, - pathways TEXT, - gene_gene_interactions TEXT, - gene_localizations TEXT, - PRIMARY KEY (genes, organisms, gene_organisms, activities, gene_functions, cellular_processes, pathways, gene_gene_interactions, gene_localizations) -); - -CREATE TABLE "MolecularActivity" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Molecule" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Organism" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Pathway" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "GeneGeneInteraction" ( - gene1 TEXT, - gene2 TEXT, - PRIMARY KEY (gene1, gene2), - FOREIGN KEY(gene1) REFERENCES "Gene" (id), - FOREIGN KEY(gene2) REFERENCES "Gene" (id) -); - -CREATE TABLE "GeneMolecularActivityRelationship" ( - gene TEXT, - molecular_activity TEXT, - PRIMARY KEY (gene, molecular_activity), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(molecular_activity) REFERENCES "MolecularActivity" (id) -); - -CREATE TABLE "GeneMolecularActivityRelationship2" ( - gene TEXT, - molecular_activity TEXT, - target TEXT, - PRIMARY KEY (gene, molecular_activity, target), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(molecular_activity) REFERENCES "MolecularActivity" (id), - FOREIGN KEY(target) REFERENCES "Molecule" (id) -); - -CREATE TABLE "GeneOrganismRelationship" ( - gene TEXT, - organism TEXT, - PRIMARY KEY (gene, organism), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(organism) REFERENCES "Organism" (id) -); - -CREATE TABLE "GeneSubcellularLocalizationRelationship" ( - gene TEXT, - location TEXT, - PRIMARY KEY (gene, location), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(location) REFERENCES "GeneLocation" (id) -); diff --git a/projects/ibd_literature/docs/AnnotatorResult.md b/projects/ibd_literature/docs/AnnotatorResult.md deleted file mode 100644 index e48de215a..000000000 --- a/projects/ibd_literature/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [ibdlit:AnnotatorResult](http://w3id.org/ontogpt/ibd_literature/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/Any.md b/projects/ibd_literature/docs/Any.md deleted file mode 100644 index 59eefc666..000000000 --- a/projects/ibd_literature/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [ibdlit:Any](http://w3id.org/ontogpt/ibd_literature/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/ibd_literature/docs/CellularProcess.md b/projects/ibd_literature/docs/CellularProcess.md deleted file mode 100644 index 38723e647..000000000 --- a/projects/ibd_literature/docs/CellularProcess.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: CellularProcess - - - - -URI: [ibdlit:CellularProcess](http://w3id.org/ontogpt/ibd_literature/CellularProcess) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiseaseCellularProcessRelationship],[DiseaseCellularProcessRelationship]-%20object%200..1>[CellularProcess|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20cellular_process%200..*>[CellularProcess],[NamedEntity]^-[CellularProcess],[IBDAnnotations])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiseaseCellularProcessRelationship],[DiseaseCellularProcessRelationship]-%20object%200..1>[CellularProcess|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20cellular_process%200..*>[CellularProcess],[NamedEntity]^-[CellularProcess],[IBDAnnotations]) - -## Identifier prefixes - - * GO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md)** *[DiseaseCellularProcessRelationship➞object](DiseaseCellularProcessRelationship_object.md)* <sub>0..1</sub> **[CellularProcess](CellularProcess.md)** - * **None** *[➞cellular_process](iBDAnnotations__cellular_process.md)* <sub>0..\*</sub> **[CellularProcess](CellularProcess.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/ChemicalExposure.md b/projects/ibd_literature/docs/ChemicalExposure.md deleted file mode 100644 index 72660bf7b..000000000 --- a/projects/ibd_literature/docs/ChemicalExposure.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Class: ChemicalExposure - - - - -URI: [ibdlit:ChemicalExposure](http://w3id.org/ontogpt/ibd_literature/ChemicalExposure) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneExposureRelationship],[GeneExposureRelationship]-%20subject%200..1>[ChemicalExposure|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20exposures%200..*>[ChemicalExposure],[NamedEntity]^-[ChemicalExposure],[IBDAnnotations])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneExposureRelationship],[GeneExposureRelationship]-%20subject%200..1>[ChemicalExposure|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20exposures%200..*>[ChemicalExposure],[NamedEntity]^-[ChemicalExposure],[IBDAnnotations]) - -## Identifier prefixes - - * CHEBI - * ECTO - * ExO - * NCIT - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[GeneExposureRelationship](GeneExposureRelationship.md)** *[GeneExposureRelationship➞subject](GeneExposureRelationship_subject.md)* <sub>0..1</sub> **[ChemicalExposure](ChemicalExposure.md)** - * **None** *[➞exposures](iBDAnnotations__exposures.md)* <sub>0..\*</sub> **[ChemicalExposure](ChemicalExposure.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/ChemicalExposureToGenePredicate.md b/projects/ibd_literature/docs/ChemicalExposureToGenePredicate.md deleted file mode 100644 index a9803ac2d..000000000 --- a/projects/ibd_literature/docs/ChemicalExposureToGenePredicate.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: ChemicalExposureToGenePredicate - - - - -URI: [ibdlit:ChemicalExposureToGenePredicate](http://w3id.org/ontogpt/ibd_literature/ChemicalExposureToGenePredicate) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[GeneExposureRelationship],[GeneExposureRelationship]-%20predicate%200..1>[ChemicalExposureToGenePredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ChemicalExposureToGenePredicate])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[GeneExposureRelationship],[GeneExposureRelationship]-%20predicate%200..1>[ChemicalExposureToGenePredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[ChemicalExposureToGenePredicate]) - -## Identifier prefixes - - * RO - -## Parents - - * is_a: [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **[GeneExposureRelationship](GeneExposureRelationship.md)** *[GeneExposureRelationship➞predicate](GeneExposureRelationship_predicate.md)* <sub>0..1</sub> **[ChemicalExposureToGenePredicate](ChemicalExposureToGenePredicate.md)** - -## Attributes - - -### Inherited from RelationshipType: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/CompoundExpression.md b/projects/ibd_literature/docs/CompoundExpression.md deleted file mode 100644 index ef1ec548e..000000000 --- a/projects/ibd_literature/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [ibdlit:CompoundExpression](http://w3id.org/ontogpt/ibd_literature/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/ibd_literature/docs/Disease.md b/projects/ibd_literature/docs/Disease.md deleted file mode 100644 index a04546e69..000000000 --- a/projects/ibd_literature/docs/Disease.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Disease - - - - -URI: [ibdlit:Disease](http://w3id.org/ontogpt/ibd_literature/Disease) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiseaseCellularProcessRelationship],[DiseaseCellularProcessRelationship]-%20subject%200..1>[Disease|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20diseases%200..*>[Disease],[NamedEntity]^-[Disease],[IBDAnnotations])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiseaseCellularProcessRelationship],[DiseaseCellularProcessRelationship]-%20subject%200..1>[Disease|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20diseases%200..*>[Disease],[NamedEntity]^-[Disease],[IBDAnnotations]) - -## Identifier prefixes - - * MONDO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md)** *[DiseaseCellularProcessRelationship➞subject](DiseaseCellularProcessRelationship_subject.md)* <sub>0..1</sub> **[Disease](Disease.md)** - * **None** *[➞diseases](iBDAnnotations__diseases.md)* <sub>0..\*</sub> **[Disease](Disease.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship.md b/projects/ibd_literature/docs/DiseaseCellularProcessRelationship.md deleted file mode 100644 index 066009c74..000000000 --- a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship.md +++ /dev/null @@ -1,43 +0,0 @@ - -# Class: DiseaseCellularProcessRelationship - - - - -URI: [ibdlit:DiseaseCellularProcessRelationship](http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[NamedEntity],[DiseaseToCellularProcessPredicate],[NamedEntity]<object_qualifier%200..1-%20[DiseaseCellularProcessRelationship|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[DiseaseCellularProcessRelationship],[CellularProcess]<object%200..1-%20[DiseaseCellularProcessRelationship],[DiseaseToCellularProcessPredicate]<predicate%200..1-%20[DiseaseCellularProcessRelationship],[Disease]<subject%200..1-%20[DiseaseCellularProcessRelationship],[IBDAnnotations]++-%20disease_cellular_process_relationships%200..*>[DiseaseCellularProcessRelationship],[Triple]^-[DiseaseCellularProcessRelationship],[IBDAnnotations],[Disease],[CellularProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[NamedEntity],[DiseaseToCellularProcessPredicate],[NamedEntity]<object_qualifier%200..1-%20[DiseaseCellularProcessRelationship|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[DiseaseCellularProcessRelationship],[CellularProcess]<object%200..1-%20[DiseaseCellularProcessRelationship],[DiseaseToCellularProcessPredicate]<predicate%200..1-%20[DiseaseCellularProcessRelationship],[Disease]<subject%200..1-%20[DiseaseCellularProcessRelationship],[IBDAnnotations]++-%20disease_cellular_process_relationships%200..*>[DiseaseCellularProcessRelationship],[Triple]^-[DiseaseCellularProcessRelationship],[IBDAnnotations],[Disease],[CellularProcess]) - -## Parents - - * is_a: [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - * **None** *[➞disease_cellular_process_relationships](iBDAnnotations__disease_cellular_process_relationships.md)* <sub>0..\*</sub> **[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md)** - -## Attributes - - -### Own - - * [DiseaseCellularProcessRelationship➞subject](DiseaseCellularProcessRelationship_subject.md) <sub>0..1</sub> - * Description: The name of the disease. - * Range: [Disease](Disease.md) - * [DiseaseCellularProcessRelationship➞predicate](DiseaseCellularProcessRelationship_predicate.md) <sub>0..1</sub> - * Description: The name of the type of relationship between a disease and a cellular process. - * Range: [DiseaseToCellularProcessPredicate](DiseaseToCellularProcessPredicate.md) - * [DiseaseCellularProcessRelationship➞object](DiseaseCellularProcessRelationship_object.md) <sub>0..1</sub> - * Description: The name of the cellular process. - * Range: [CellularProcess](CellularProcess.md) - * [DiseaseCellularProcessRelationship➞subject_qualifier](DiseaseCellularProcessRelationship_subject_qualifier.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [DiseaseCellularProcessRelationship➞object_qualifier](DiseaseCellularProcessRelationship_object_qualifier.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - -### Inherited from Triple: - - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_object.md b/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_object.md deleted file mode 100644 index 3c273b6d5..000000000 --- a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_object.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object - - -The name of the cellular process. - -URI: [ibdlit:DiseaseCellularProcessRelationship_object](http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship_object) - - -## Domain and Range - -[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) → <sub>0..1</sub> [CellularProcess](CellularProcess.md) - -## Parents - - * is_a: [➞object](triple__object.md) - -## Children - - -## Used by - - * [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) diff --git a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_object_qualifier.md b/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_object_qualifier.md deleted file mode 100644 index b1f396ac3..000000000 --- a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_object_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object_qualifier - - - - -URI: [ibdlit:DiseaseCellularProcessRelationship_object_qualifier](http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship_object_qualifier) - - -## Domain and Range - -[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞object_qualifier](triple__object_qualifier.md) - -## Children - - -## Used by - - * [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) diff --git a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_predicate.md b/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_predicate.md deleted file mode 100644 index 01b2758cf..000000000 --- a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_predicate.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: predicate - - -The name of the type of relationship between a disease and a cellular process. - -URI: [ibdlit:DiseaseCellularProcessRelationship_predicate](http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship_predicate) - - -## Domain and Range - -[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) → <sub>0..1</sub> [DiseaseToCellularProcessPredicate](DiseaseToCellularProcessPredicate.md) - -## Parents - - * is_a: [➞predicate](triple__predicate.md) - -## Children - - -## Used by - - * [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) diff --git a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_subject.md b/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_subject.md deleted file mode 100644 index b0dd129a7..000000000 --- a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_subject.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject - - -The name of the disease. - -URI: [ibdlit:DiseaseCellularProcessRelationship_subject](http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship_subject) - - -## Domain and Range - -[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) → <sub>0..1</sub> [Disease](Disease.md) - -## Parents - - * is_a: [➞subject](triple__subject.md) - -## Children - - -## Used by - - * [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) diff --git a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_subject_qualifier.md b/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_subject_qualifier.md deleted file mode 100644 index eea72a153..000000000 --- a/projects/ibd_literature/docs/DiseaseCellularProcessRelationship_subject_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject_qualifier - - - - -URI: [ibdlit:DiseaseCellularProcessRelationship_subject_qualifier](http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship_subject_qualifier) - - -## Domain and Range - -[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞subject_qualifier](triple__subject_qualifier.md) - -## Children - - -## Used by - - * [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) diff --git a/projects/ibd_literature/docs/DiseaseToCellularProcessPredicate.md b/projects/ibd_literature/docs/DiseaseToCellularProcessPredicate.md deleted file mode 100644 index c35926d70..000000000 --- a/projects/ibd_literature/docs/DiseaseToCellularProcessPredicate.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: DiseaseToCellularProcessPredicate - - - - -URI: [ibdlit:DiseaseToCellularProcessPredicate](http://w3id.org/ontogpt/ibd_literature/DiseaseToCellularProcessPredicate) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[DiseaseCellularProcessRelationship]-%20predicate%200..1>[DiseaseToCellularProcessPredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[DiseaseToCellularProcessPredicate],[DiseaseCellularProcessRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[DiseaseCellularProcessRelationship]-%20predicate%200..1>[DiseaseToCellularProcessPredicate|id(i):string;label(i):string%20%3F],[RelationshipType]^-[DiseaseToCellularProcessPredicate],[DiseaseCellularProcessRelationship]) - -## Identifier prefixes - - * RO - -## Parents - - * is_a: [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md)** *[DiseaseCellularProcessRelationship➞predicate](DiseaseCellularProcessRelationship_predicate.md)* <sub>0..1</sub> **[DiseaseToCellularProcessPredicate](DiseaseToCellularProcessPredicate.md)** - -## Attributes - - -### Inherited from RelationshipType: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/ExtractionResult.md b/projects/ibd_literature/docs/ExtractionResult.md deleted file mode 100644 index b6fb00ea8..000000000 --- a/projects/ibd_literature/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [ibdlit:ExtractionResult](http://w3id.org/ontogpt/ibd_literature/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/ibd_literature/docs/Gene.md b/projects/ibd_literature/docs/Gene.md deleted file mode 100644 index 6cfdb829f..000000000 --- a/projects/ibd_literature/docs/Gene.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Gene - - - - -URI: [ibdlit:Gene](http://w3id.org/ontogpt/ibd_literature/Gene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneExposureRelationship],[GeneExposureRelationship]-%20object%200..1>[Gene|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20genes%200..*>[Gene],[NamedEntity]^-[Gene],[IBDAnnotations])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneExposureRelationship],[GeneExposureRelationship]-%20object%200..1>[Gene|id(i):string;label(i):string%20%3F],[IBDAnnotations]-%20genes%200..*>[Gene],[NamedEntity]^-[Gene],[IBDAnnotations]) - -## Identifier prefixes - - * HGNC - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **[GeneExposureRelationship](GeneExposureRelationship.md)** *[GeneExposureRelationship➞object](GeneExposureRelationship_object.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞genes](iBDAnnotations__genes.md)* <sub>0..\*</sub> **[Gene](Gene.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/GeneExposureRelationship.md b/projects/ibd_literature/docs/GeneExposureRelationship.md deleted file mode 100644 index b4875649b..000000000 --- a/projects/ibd_literature/docs/GeneExposureRelationship.md +++ /dev/null @@ -1,45 +0,0 @@ - -# Class: GeneExposureRelationship - - - - -URI: [ibdlit:GeneExposureRelationship](http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[NamedEntity],[NamedEntity]<object_qualifier%200..1-%20[GeneExposureRelationship|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[GeneExposureRelationship],[Gene]<object%200..1-%20[GeneExposureRelationship],[ChemicalExposureToGenePredicate]<predicate%200..1-%20[GeneExposureRelationship],[ChemicalExposure]<subject%200..1-%20[GeneExposureRelationship],[IBDAnnotations]++-%20gene_exposures_relationships%200..*>[GeneExposureRelationship],[Triple]^-[GeneExposureRelationship],[IBDAnnotations],[Gene],[ChemicalExposureToGenePredicate],[ChemicalExposure])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[NamedEntity],[NamedEntity]<object_qualifier%200..1-%20[GeneExposureRelationship|qualifier(i):string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[GeneExposureRelationship],[Gene]<object%200..1-%20[GeneExposureRelationship],[ChemicalExposureToGenePredicate]<predicate%200..1-%20[GeneExposureRelationship],[ChemicalExposure]<subject%200..1-%20[GeneExposureRelationship],[IBDAnnotations]++-%20gene_exposures_relationships%200..*>[GeneExposureRelationship],[Triple]^-[GeneExposureRelationship],[IBDAnnotations],[Gene],[ChemicalExposureToGenePredicate],[ChemicalExposure]) - -## Parents - - * is_a: [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - * **None** *[➞gene_exposures_relationships](iBDAnnotations__gene_exposures_relationships.md)* <sub>0..\*</sub> **[GeneExposureRelationship](GeneExposureRelationship.md)** - -## Attributes - - -### Own - - * [GeneExposureRelationship➞subject](GeneExposureRelationship_subject.md) <sub>0..1</sub> - * Description: The name of the exposure, such as a exposure to a chemical toxin. - * Range: [ChemicalExposure](ChemicalExposure.md) - * [GeneExposureRelationship➞predicate](GeneExposureRelationship_predicate.md) <sub>0..1</sub> - * Description: The name of the type of relationship between a chemical exposure and a gene. - * Range: [ChemicalExposureToGenePredicate](ChemicalExposureToGenePredicate.md) - * [GeneExposureRelationship➞object](GeneExposureRelationship_object.md) <sub>0..1</sub> - * Description: The name of the gene in the pair. This comes second in the pair. - * Range: [Gene](Gene.md) - * [GeneExposureRelationship➞subject_qualifier](GeneExposureRelationship_subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the chemical exposure. - * Range: [NamedEntity](NamedEntity.md) - * [GeneExposureRelationship➞object_qualifier](GeneExposureRelationship_object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the gene. - * Range: [NamedEntity](NamedEntity.md) - -### Inherited from Triple: - - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/GeneExposureRelationship_object.md b/projects/ibd_literature/docs/GeneExposureRelationship_object.md deleted file mode 100644 index 89f0b83ae..000000000 --- a/projects/ibd_literature/docs/GeneExposureRelationship_object.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object - - -The name of the gene in the pair. This comes second in the pair. - -URI: [ibdlit:GeneExposureRelationship_object](http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship_object) - - -## Domain and Range - -[GeneExposureRelationship](GeneExposureRelationship.md) → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - * is_a: [➞object](triple__object.md) - -## Children - - -## Used by - - * [GeneExposureRelationship](GeneExposureRelationship.md) diff --git a/projects/ibd_literature/docs/GeneExposureRelationship_object_qualifier.md b/projects/ibd_literature/docs/GeneExposureRelationship_object_qualifier.md deleted file mode 100644 index 05f97900a..000000000 --- a/projects/ibd_literature/docs/GeneExposureRelationship_object_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the gene. - -URI: [ibdlit:GeneExposureRelationship_object_qualifier](http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship_object_qualifier) - - -## Domain and Range - -[GeneExposureRelationship](GeneExposureRelationship.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞object_qualifier](triple__object_qualifier.md) - -## Children - - -## Used by - - * [GeneExposureRelationship](GeneExposureRelationship.md) diff --git a/projects/ibd_literature/docs/GeneExposureRelationship_predicate.md b/projects/ibd_literature/docs/GeneExposureRelationship_predicate.md deleted file mode 100644 index 50e7c9169..000000000 --- a/projects/ibd_literature/docs/GeneExposureRelationship_predicate.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: predicate - - -The name of the type of relationship between a chemical exposure and a gene. - -URI: [ibdlit:GeneExposureRelationship_predicate](http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship_predicate) - - -## Domain and Range - -[GeneExposureRelationship](GeneExposureRelationship.md) → <sub>0..1</sub> [ChemicalExposureToGenePredicate](ChemicalExposureToGenePredicate.md) - -## Parents - - * is_a: [➞predicate](triple__predicate.md) - -## Children - - -## Used by - - * [GeneExposureRelationship](GeneExposureRelationship.md) diff --git a/projects/ibd_literature/docs/GeneExposureRelationship_subject.md b/projects/ibd_literature/docs/GeneExposureRelationship_subject.md deleted file mode 100644 index af1cf060d..000000000 --- a/projects/ibd_literature/docs/GeneExposureRelationship_subject.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject - - -The name of the exposure, such as a exposure to a chemical toxin. - -URI: [ibdlit:GeneExposureRelationship_subject](http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship_subject) - - -## Domain and Range - -[GeneExposureRelationship](GeneExposureRelationship.md) → <sub>0..1</sub> [ChemicalExposure](ChemicalExposure.md) - -## Parents - - * is_a: [➞subject](triple__subject.md) - -## Children - - -## Used by - - * [GeneExposureRelationship](GeneExposureRelationship.md) diff --git a/projects/ibd_literature/docs/GeneExposureRelationship_subject_qualifier.md b/projects/ibd_literature/docs/GeneExposureRelationship_subject_qualifier.md deleted file mode 100644 index b6dd16f4d..000000000 --- a/projects/ibd_literature/docs/GeneExposureRelationship_subject_qualifier.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the chemical exposure. - -URI: [ibdlit:GeneExposureRelationship_subject_qualifier](http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship_subject_qualifier) - - -## Domain and Range - -[GeneExposureRelationship](GeneExposureRelationship.md) → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - * is_a: [➞subject_qualifier](triple__subject_qualifier.md) - -## Children - - -## Used by - - * [GeneExposureRelationship](GeneExposureRelationship.md) diff --git a/projects/ibd_literature/docs/IBDAnnotations.md b/projects/ibd_literature/docs/IBDAnnotations.md deleted file mode 100644 index 512cc59ce..000000000 --- a/projects/ibd_literature/docs/IBDAnnotations.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: IBDAnnotations - - - - -URI: [ibdlit:IBDAnnotations](http://w3id.org/ontogpt/ibd_literature/IBDAnnotations) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[DiseaseCellularProcessRelationship]<disease_cellular_process_relationships%200..*-++[IBDAnnotations],[CellularProcess]<cellular_process%200..*-%20[IBDAnnotations],[Disease]<diseases%200..*-%20[IBDAnnotations],[GeneExposureRelationship]<gene_exposures_relationships%200..*-++[IBDAnnotations],[ChemicalExposure]<exposures%200..*-%20[IBDAnnotations],[Gene]<genes%200..*-%20[IBDAnnotations],[GeneExposureRelationship],[Gene],[DiseaseCellularProcessRelationship],[Disease],[ChemicalExposure],[CellularProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[DiseaseCellularProcessRelationship]<disease_cellular_process_relationships%200..*-++[IBDAnnotations],[CellularProcess]<cellular_process%200..*-%20[IBDAnnotations],[Disease]<diseases%200..*-%20[IBDAnnotations],[GeneExposureRelationship]<gene_exposures_relationships%200..*-++[IBDAnnotations],[ChemicalExposure]<exposures%200..*-%20[IBDAnnotations],[Gene]<genes%200..*-%20[IBDAnnotations],[GeneExposureRelationship],[Gene],[DiseaseCellularProcessRelationship],[Disease],[ChemicalExposure],[CellularProcess]) - -## Attributes - - -### Own - - * [➞genes](iBDAnnotations__genes.md) <sub>0..\*</sub> - * Description: semicolon-separated list of genes - * Range: [Gene](Gene.md) - * [➞exposures](iBDAnnotations__exposures.md) <sub>0..\*</sub> - * Description: semicolon-separated list of exposures - * Range: [ChemicalExposure](ChemicalExposure.md) - * [➞gene_exposures_relationships](iBDAnnotations__gene_exposures_relationships.md) <sub>0..\*</sub> - * Description: semicolon-separated list of gene to molecular activity relationships - * Range: [GeneExposureRelationship](GeneExposureRelationship.md) - * [➞diseases](iBDAnnotations__diseases.md) <sub>0..\*</sub> - * Description: semicolon-separated list of diseases - * Range: [Disease](Disease.md) - * [➞cellular_process](iBDAnnotations__cellular_process.md) <sub>0..\*</sub> - * Description: semicolon-separated list of cellular processes - * Range: [CellularProcess](CellularProcess.md) - * [➞disease_cellular_process_relationships](iBDAnnotations__disease_cellular_process_relationships.md) <sub>0..\*</sub> - * Description: semicolon-separated list of disease to cellular process relationships - * Range: [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) diff --git a/projects/ibd_literature/docs/NamedEntity.md b/projects/ibd_literature/docs/NamedEntity.md deleted file mode 100644 index 7735e30cf..000000000 --- a/projects/ibd_literature/docs/NamedEntity.md +++ /dev/null @@ -1,41 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [ibdlit:NamedEntity](http://w3id.org/ontogpt/ibd_literature/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[DiseaseCellularProcessRelationship]-%20object_qualifier%200..1>[NamedEntity|id:string;label:string%20%3F],[DiseaseCellularProcessRelationship]-%20subject_qualifier%200..1>[NamedEntity],[GeneExposureRelationship]-%20object_qualifier%200..1>[NamedEntity],[GeneExposureRelationship]-%20subject_qualifier%200..1>[NamedEntity],[Triple]-%20object%200..1>[NamedEntity],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Gene],[NamedEntity]^-[Disease],[NamedEntity]^-[ChemicalExposure],[NamedEntity]^-[CellularProcess],[Triple],[GeneExposureRelationship],[Gene],[DiseaseCellularProcessRelationship],[Disease],[ChemicalExposure],[CellularProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[DiseaseCellularProcessRelationship]-%20object_qualifier%200..1>[NamedEntity|id:string;label:string%20%3F],[DiseaseCellularProcessRelationship]-%20subject_qualifier%200..1>[NamedEntity],[GeneExposureRelationship]-%20object_qualifier%200..1>[NamedEntity],[GeneExposureRelationship]-%20subject_qualifier%200..1>[NamedEntity],[Triple]-%20object%200..1>[NamedEntity],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Gene],[NamedEntity]^-[Disease],[NamedEntity]^-[ChemicalExposure],[NamedEntity]^-[CellularProcess],[Triple],[GeneExposureRelationship],[Gene],[DiseaseCellularProcessRelationship],[Disease],[ChemicalExposure],[CellularProcess]) - -## Children - - * [CellularProcess](CellularProcess.md) - * [ChemicalExposure](ChemicalExposure.md) - * [Disease](Disease.md) - * [Gene](Gene.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md)** *[DiseaseCellularProcessRelationship➞object_qualifier](DiseaseCellularProcessRelationship_object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **[DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md)** *[DiseaseCellularProcessRelationship➞subject_qualifier](DiseaseCellularProcessRelationship_subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **[GeneExposureRelationship](GeneExposureRelationship.md)** *[GeneExposureRelationship➞object_qualifier](GeneExposureRelationship_object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **[GeneExposureRelationship](GeneExposureRelationship.md)** *[GeneExposureRelationship➞subject_qualifier](GeneExposureRelationship_subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/NullDataOptions.md b/projects/ibd_literature/docs/NullDataOptions.md deleted file mode 100644 index 09063060e..000000000 --- a/projects/ibd_literature/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [ibdlit:NullDataOptions](http://w3id.org/ontogpt/ibd_literature/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/ibd_literature/docs/Publication.md b/projects/ibd_literature/docs/Publication.md deleted file mode 100644 index c5d4a3ac0..000000000 --- a/projects/ibd_literature/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [ibdlit:Publication](http://w3id.org/ontogpt/ibd_literature/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/RelationshipType.md b/projects/ibd_literature/docs/RelationshipType.md deleted file mode 100644 index cdf14db38..000000000 --- a/projects/ibd_literature/docs/RelationshipType.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [ibdlit:RelationshipType](http://w3id.org/ontogpt/ibd_literature/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[RelationshipType]^-[DiseaseToCellularProcessPredicate],[RelationshipType]^-[ChemicalExposureToGenePredicate],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity],[DiseaseToCellularProcessPredicate],[ChemicalExposureToGenePredicate])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[RelationshipType]^-[DiseaseToCellularProcessPredicate],[RelationshipType]^-[ChemicalExposureToGenePredicate],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity],[DiseaseToCellularProcessPredicate],[ChemicalExposureToGenePredicate]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Children - - * [ChemicalExposureToGenePredicate](ChemicalExposureToGenePredicate.md) - * [DiseaseToCellularProcessPredicate](DiseaseToCellularProcessPredicate.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ibd_literature/docs/TextWithTriples.md b/projects/ibd_literature/docs/TextWithTriples.md deleted file mode 100644 index ef6237a45..000000000 --- a/projects/ibd_literature/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [ibdlit:TextWithTriples](http://w3id.org/ontogpt/ibd_literature/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/ibd_literature/docs/Triple.md b/projects/ibd_literature/docs/Triple.md deleted file mode 100644 index 46bc252cd..000000000 --- a/projects/ibd_literature/docs/Triple.md +++ /dev/null @@ -1,44 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [ibdlit:Triple](http://w3id.org/ontogpt/ibd_literature/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[Triple]^-[GeneExposureRelationship],[Triple]^-[DiseaseCellularProcessRelationship],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[GeneExposureRelationship],[DiseaseCellularProcessRelationship],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[Triple]^-[GeneExposureRelationship],[Triple]^-[DiseaseCellularProcessRelationship],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[GeneExposureRelationship],[DiseaseCellularProcessRelationship],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Children - - * [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) - * [GeneExposureRelationship](GeneExposureRelationship.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/ibd_literature/docs/annotatorResult__object_id.md b/projects/ibd_literature/docs/annotatorResult__object_id.md deleted file mode 100644 index 647c4bef4..000000000 --- a/projects/ibd_literature/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [ibdlit:annotatorResult__object_id](http://w3id.org/ontogpt/ibd_literature/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ibd_literature/docs/annotatorResult__object_text.md b/projects/ibd_literature/docs/annotatorResult__object_text.md deleted file mode 100644 index a30048036..000000000 --- a/projects/ibd_literature/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [ibdlit:annotatorResult__object_text](http://w3id.org/ontogpt/ibd_literature/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ibd_literature/docs/annotatorResult__subject_text.md b/projects/ibd_literature/docs/annotatorResult__subject_text.md deleted file mode 100644 index 2c4f1c51d..000000000 --- a/projects/ibd_literature/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [ibdlit:annotatorResult__subject_text](http://w3id.org/ontogpt/ibd_literature/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ibd_literature/docs/extractionResult__extracted_object.md b/projects/ibd_literature/docs/extractionResult__extracted_object.md deleted file mode 100644 index 5d30c7a28..000000000 --- a/projects/ibd_literature/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [ibdlit:extractionResult__extracted_object](http://w3id.org/ontogpt/ibd_literature/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd_literature/docs/extractionResult__input_id.md b/projects/ibd_literature/docs/extractionResult__input_id.md deleted file mode 100644 index 9a04136bb..000000000 --- a/projects/ibd_literature/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [ibdlit:extractionResult__input_id](http://w3id.org/ontogpt/ibd_literature/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd_literature/docs/extractionResult__input_text.md b/projects/ibd_literature/docs/extractionResult__input_text.md deleted file mode 100644 index 599caca0d..000000000 --- a/projects/ibd_literature/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [ibdlit:extractionResult__input_text](http://w3id.org/ontogpt/ibd_literature/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd_literature/docs/extractionResult__input_title.md b/projects/ibd_literature/docs/extractionResult__input_title.md deleted file mode 100644 index c22ea8d69..000000000 --- a/projects/ibd_literature/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [ibdlit:extractionResult__input_title](http://w3id.org/ontogpt/ibd_literature/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd_literature/docs/extractionResult__named_entities.md b/projects/ibd_literature/docs/extractionResult__named_entities.md deleted file mode 100644 index 0aa94909b..000000000 --- a/projects/ibd_literature/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [ibdlit:extractionResult__named_entities](http://w3id.org/ontogpt/ibd_literature/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd_literature/docs/extractionResult__prompt.md b/projects/ibd_literature/docs/extractionResult__prompt.md deleted file mode 100644 index 22dde1c30..000000000 --- a/projects/ibd_literature/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [ibdlit:extractionResult__prompt](http://w3id.org/ontogpt/ibd_literature/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd_literature/docs/extractionResult__raw_completion_output.md b/projects/ibd_literature/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 3ca6095de..000000000 --- a/projects/ibd_literature/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [ibdlit:extractionResult__raw_completion_output](http://w3id.org/ontogpt/ibd_literature/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ibd_literature/docs/iBDAnnotations__cellular_process.md b/projects/ibd_literature/docs/iBDAnnotations__cellular_process.md deleted file mode 100644 index d35161fef..000000000 --- a/projects/ibd_literature/docs/iBDAnnotations__cellular_process.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: cellular_process - - -semicolon-separated list of cellular processes - -URI: [ibdlit:iBDAnnotations__cellular_process](http://w3id.org/ontogpt/ibd_literature/iBDAnnotations__cellular_process) - - -## Domain and Range - -None → <sub>0..\*</sub> [CellularProcess](CellularProcess.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd_literature/docs/iBDAnnotations__disease_cellular_process_relationships.md b/projects/ibd_literature/docs/iBDAnnotations__disease_cellular_process_relationships.md deleted file mode 100644 index 03eafa9e3..000000000 --- a/projects/ibd_literature/docs/iBDAnnotations__disease_cellular_process_relationships.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: disease_cellular_process_relationships - - -semicolon-separated list of disease to cellular process relationships - -URI: [ibdlit:iBDAnnotations__disease_cellular_process_relationships](http://w3id.org/ontogpt/ibd_literature/iBDAnnotations__disease_cellular_process_relationships) - - -## Domain and Range - -None → <sub>0..\*</sub> [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd_literature/docs/iBDAnnotations__diseases.md b/projects/ibd_literature/docs/iBDAnnotations__diseases.md deleted file mode 100644 index 46e81faa0..000000000 --- a/projects/ibd_literature/docs/iBDAnnotations__diseases.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: diseases - - -semicolon-separated list of diseases - -URI: [ibdlit:iBDAnnotations__diseases](http://w3id.org/ontogpt/ibd_literature/iBDAnnotations__diseases) - - -## Domain and Range - -None → <sub>0..\*</sub> [Disease](Disease.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd_literature/docs/iBDAnnotations__exposures.md b/projects/ibd_literature/docs/iBDAnnotations__exposures.md deleted file mode 100644 index bfec6310a..000000000 --- a/projects/ibd_literature/docs/iBDAnnotations__exposures.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: exposures - - -semicolon-separated list of exposures - -URI: [ibdlit:iBDAnnotations__exposures](http://w3id.org/ontogpt/ibd_literature/iBDAnnotations__exposures) - - -## Domain and Range - -None → <sub>0..\*</sub> [ChemicalExposure](ChemicalExposure.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd_literature/docs/iBDAnnotations__gene_exposures_relationships.md b/projects/ibd_literature/docs/iBDAnnotations__gene_exposures_relationships.md deleted file mode 100644 index d51ac65b5..000000000 --- a/projects/ibd_literature/docs/iBDAnnotations__gene_exposures_relationships.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_exposures_relationships - - -semicolon-separated list of gene to molecular activity relationships - -URI: [ibdlit:iBDAnnotations__gene_exposures_relationships](http://w3id.org/ontogpt/ibd_literature/iBDAnnotations__gene_exposures_relationships) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneExposureRelationship](GeneExposureRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd_literature/docs/iBDAnnotations__genes.md b/projects/ibd_literature/docs/iBDAnnotations__genes.md deleted file mode 100644 index 4ae8dc48c..000000000 --- a/projects/ibd_literature/docs/iBDAnnotations__genes.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: genes - - -semicolon-separated list of genes - -URI: [ibdlit:iBDAnnotations__genes](http://w3id.org/ontogpt/ibd_literature/iBDAnnotations__genes) - - -## Domain and Range - -None → <sub>0..\*</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [IBDAnnotations](IBDAnnotations.md) diff --git a/projects/ibd_literature/docs/ibd_literature.md b/projects/ibd_literature/docs/ibd_literature.md deleted file mode 100644 index 6b57fc3a7..000000000 --- a/projects/ibd_literature/docs/ibd_literature.md +++ /dev/null @@ -1,128 +0,0 @@ - -# ibd-literature-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for extracting information from IBD literature - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) - * [GeneExposureRelationship](GeneExposureRelationship.md) - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [IBDAnnotations](IBDAnnotations.md) - * [NamedEntity](NamedEntity.md) - * [CellularProcess](CellularProcess.md) - * [ChemicalExposure](ChemicalExposure.md) - * [Disease](Disease.md) - * [Gene](Gene.md) - * [RelationshipType](RelationshipType.md) - * [ChemicalExposureToGenePredicate](ChemicalExposureToGenePredicate.md) - * [DiseaseToCellularProcessPredicate](DiseaseToCellularProcessPredicate.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞cellular_process](iBDAnnotations__cellular_process.md) - semicolon-separated list of cellular processes - * [➞disease_cellular_process_relationships](iBDAnnotations__disease_cellular_process_relationships.md) - semicolon-separated list of disease to cellular process relationships - * [➞diseases](iBDAnnotations__diseases.md) - semicolon-separated list of diseases - * [➞exposures](iBDAnnotations__exposures.md) - semicolon-separated list of exposures - * [➞gene_exposures_relationships](iBDAnnotations__gene_exposures_relationships.md) - semicolon-separated list of gene to molecular activity relationships - * [➞genes](iBDAnnotations__genes.md) - semicolon-separated list of genes - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [DiseaseCellularProcessRelationship➞object](DiseaseCellularProcessRelationship_object.md) - The name of the cellular process. - * [GeneExposureRelationship➞object](GeneExposureRelationship_object.md) - The name of the gene in the pair. This comes second in the pair. - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [DiseaseCellularProcessRelationship➞object_qualifier](DiseaseCellularProcessRelationship_object_qualifier.md) - * [GeneExposureRelationship➞object_qualifier](GeneExposureRelationship_object_qualifier.md) - An optional qualifier or modifier for the gene. - * [➞predicate](triple__predicate.md) - * [DiseaseCellularProcessRelationship➞predicate](DiseaseCellularProcessRelationship_predicate.md) - The name of the type of relationship between a disease and a cellular process. - * [GeneExposureRelationship➞predicate](GeneExposureRelationship_predicate.md) - The name of the type of relationship between a chemical exposure and a gene. - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [DiseaseCellularProcessRelationship➞subject](DiseaseCellularProcessRelationship_subject.md) - The name of the disease. - * [GeneExposureRelationship➞subject](GeneExposureRelationship_subject.md) - The name of the exposure, such as a exposure to a chemical toxin. - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * [DiseaseCellularProcessRelationship➞subject_qualifier](DiseaseCellularProcessRelationship_subject_qualifier.md) - * [GeneExposureRelationship➞subject_qualifier](GeneExposureRelationship_subject_qualifier.md) - An optional qualifier or modifier for the chemical exposure. - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/ibd_literature/docs/namedEntity__id.md b/projects/ibd_literature/docs/namedEntity__id.md deleted file mode 100644 index 97e6173e8..000000000 --- a/projects/ibd_literature/docs/namedEntity__id.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [ibdlit:namedEntity__id](http://w3id.org/ontogpt/ibd_literature/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [CellularProcess](CellularProcess.md) - * [ChemicalExposure](ChemicalExposure.md) - * [ChemicalExposureToGenePredicate](ChemicalExposureToGenePredicate.md) - * [Disease](Disease.md) - * [DiseaseToCellularProcessPredicate](DiseaseToCellularProcessPredicate.md) - * [Gene](Gene.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/ibd_literature/docs/namedEntity__label.md b/projects/ibd_literature/docs/namedEntity__label.md deleted file mode 100644 index b9b4b4f60..000000000 --- a/projects/ibd_literature/docs/namedEntity__label.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [ibdlit:namedEntity__label](http://w3id.org/ontogpt/ibd_literature/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [CellularProcess](CellularProcess.md) - * [ChemicalExposure](ChemicalExposure.md) - * [ChemicalExposureToGenePredicate](ChemicalExposureToGenePredicate.md) - * [Disease](Disease.md) - * [DiseaseToCellularProcessPredicate](DiseaseToCellularProcessPredicate.md) - * [Gene](Gene.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/ibd_literature/docs/publication__abstract.md b/projects/ibd_literature/docs/publication__abstract.md deleted file mode 100644 index eaf627af0..000000000 --- a/projects/ibd_literature/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [ibdlit:publication__abstract](http://w3id.org/ontogpt/ibd_literature/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd_literature/docs/publication__combined_text.md b/projects/ibd_literature/docs/publication__combined_text.md deleted file mode 100644 index a6b2a61f8..000000000 --- a/projects/ibd_literature/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [ibdlit:publication__combined_text](http://w3id.org/ontogpt/ibd_literature/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd_literature/docs/publication__full_text.md b/projects/ibd_literature/docs/publication__full_text.md deleted file mode 100644 index 76e3d9016..000000000 --- a/projects/ibd_literature/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [ibdlit:publication__full_text](http://w3id.org/ontogpt/ibd_literature/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd_literature/docs/publication__id.md b/projects/ibd_literature/docs/publication__id.md deleted file mode 100644 index eb1c6ea60..000000000 --- a/projects/ibd_literature/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [ibdlit:publication__id](http://w3id.org/ontogpt/ibd_literature/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd_literature/docs/publication__title.md b/projects/ibd_literature/docs/publication__title.md deleted file mode 100644 index b0fab18d3..000000000 --- a/projects/ibd_literature/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [ibdlit:publication__title](http://w3id.org/ontogpt/ibd_literature/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ibd_literature/docs/textWithTriples__publication.md b/projects/ibd_literature/docs/textWithTriples__publication.md deleted file mode 100644 index 504853293..000000000 --- a/projects/ibd_literature/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [ibdlit:textWithTriples__publication](http://w3id.org/ontogpt/ibd_literature/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ibd_literature/docs/textWithTriples__triples.md b/projects/ibd_literature/docs/textWithTriples__triples.md deleted file mode 100644 index 9e55e2553..000000000 --- a/projects/ibd_literature/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [ibdlit:textWithTriples__triples](http://w3id.org/ontogpt/ibd_literature/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ibd_literature/docs/triple__object.md b/projects/ibd_literature/docs/triple__object.md deleted file mode 100644 index cc10dbac3..000000000 --- a/projects/ibd_literature/docs/triple__object.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: object - - - - -URI: [ibdlit:triple__object](http://w3id.org/ontogpt/ibd_literature/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [DiseaseCellularProcessRelationship➞object](DiseaseCellularProcessRelationship_object.md) - * [GeneExposureRelationship➞object](GeneExposureRelationship_object.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd_literature/docs/triple__object_qualifier.md b/projects/ibd_literature/docs/triple__object_qualifier.md deleted file mode 100644 index 5d4e81ed9..000000000 --- a/projects/ibd_literature/docs/triple__object_qualifier.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [ibdlit:triple__object_qualifier](http://w3id.org/ontogpt/ibd_literature/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [DiseaseCellularProcessRelationship➞object_qualifier](DiseaseCellularProcessRelationship_object_qualifier.md) - * [GeneExposureRelationship➞object_qualifier](GeneExposureRelationship_object_qualifier.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd_literature/docs/triple__predicate.md b/projects/ibd_literature/docs/triple__predicate.md deleted file mode 100644 index 87c051c9f..000000000 --- a/projects/ibd_literature/docs/triple__predicate.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: predicate - - - - -URI: [ibdlit:triple__predicate](http://w3id.org/ontogpt/ibd_literature/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - * [DiseaseCellularProcessRelationship➞predicate](DiseaseCellularProcessRelationship_predicate.md) - * [GeneExposureRelationship➞predicate](GeneExposureRelationship_predicate.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd_literature/docs/triple__qualifier.md b/projects/ibd_literature/docs/triple__qualifier.md deleted file mode 100644 index f0f66d196..000000000 --- a/projects/ibd_literature/docs/triple__qualifier.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [ibdlit:triple__qualifier](http://w3id.org/ontogpt/ibd_literature/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseCellularProcessRelationship](DiseaseCellularProcessRelationship.md) - * [GeneExposureRelationship](GeneExposureRelationship.md) - * [Triple](Triple.md) diff --git a/projects/ibd_literature/docs/triple__subject.md b/projects/ibd_literature/docs/triple__subject.md deleted file mode 100644 index 1f71e236e..000000000 --- a/projects/ibd_literature/docs/triple__subject.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: subject - - - - -URI: [ibdlit:triple__subject](http://w3id.org/ontogpt/ibd_literature/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [DiseaseCellularProcessRelationship➞subject](DiseaseCellularProcessRelationship_subject.md) - * [GeneExposureRelationship➞subject](GeneExposureRelationship_subject.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd_literature/docs/triple__subject_qualifier.md b/projects/ibd_literature/docs/triple__subject_qualifier.md deleted file mode 100644 index 146292d1f..000000000 --- a/projects/ibd_literature/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [ibdlit:triple__subject_qualifier](http://w3id.org/ontogpt/ibd_literature/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - * [DiseaseCellularProcessRelationship➞subject_qualifier](DiseaseCellularProcessRelationship_subject_qualifier.md) - * [GeneExposureRelationship➞subject_qualifier](GeneExposureRelationship_subject_qualifier.md) - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ibd_literature/docs/types/Boolean.md b/projects/ibd_literature/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/ibd_literature/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/ibd_literature/docs/types/Curie.md b/projects/ibd_literature/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/ibd_literature/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/ibd_literature/docs/types/Date.md b/projects/ibd_literature/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/ibd_literature/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/ibd_literature/docs/types/DateOrDatetime.md b/projects/ibd_literature/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/ibd_literature/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ibd_literature/docs/types/Datetime.md b/projects/ibd_literature/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/ibd_literature/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/ibd_literature/docs/types/Decimal.md b/projects/ibd_literature/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/ibd_literature/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/ibd_literature/docs/types/Double.md b/projects/ibd_literature/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/ibd_literature/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/ibd_literature/docs/types/Float.md b/projects/ibd_literature/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/ibd_literature/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/ibd_literature/docs/types/Integer.md b/projects/ibd_literature/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/ibd_literature/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/ibd_literature/docs/types/Jsonpath.md b/projects/ibd_literature/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/ibd_literature/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ibd_literature/docs/types/Jsonpointer.md b/projects/ibd_literature/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/ibd_literature/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ibd_literature/docs/types/Ncname.md b/projects/ibd_literature/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/ibd_literature/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/ibd_literature/docs/types/Nodeidentifier.md b/projects/ibd_literature/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/ibd_literature/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/ibd_literature/docs/types/Objectidentifier.md b/projects/ibd_literature/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/ibd_literature/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/ibd_literature/docs/types/Sparqlpath.md b/projects/ibd_literature/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/ibd_literature/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ibd_literature/docs/types/String.md b/projects/ibd_literature/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/ibd_literature/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/ibd_literature/docs/types/Time.md b/projects/ibd_literature/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/ibd_literature/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/ibd_literature/docs/types/Uri.md b/projects/ibd_literature/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/ibd_literature/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/ibd_literature/docs/types/Uriorcurie.md b/projects/ibd_literature/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/ibd_literature/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/ibd_literature/excel/ibd_literature.xlsx b/projects/ibd_literature/excel/ibd_literature.xlsx deleted file mode 100644 index 8fd01e326a5a8f44ffea498eb771fbe695d95d0e..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 11677 zcmeHtWmJ~y)-Ea1-KjLbba%IugoJc=N_R>(2+}DH(ji^aCEX$2A<cQkv$snQerJ6@ 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zYmdP^>c0=Q{V$j`+{a-ab>N3G^cRd5{^Kx@dhkOH^=}wZSi*alUyAA>tq)7!UrPg? z{Z<e^T==l0{I$^P`M<aRuLASo;)m75uf?B8?ic@|ws?s1Fth%`*&}^4&&o<d0ta<L SKrn$nSio<Vz>!@LkpBaMKdA5k diff --git a/projects/ibd_literature/graphql/ibd_literature.graphql b/projects/ibd_literature/graphql/ibd_literature.graphql deleted file mode 100644 index d894e4177..000000000 --- a/projects/ibd_literature/graphql/ibd_literature.graphql +++ /dev/null @@ -1,129 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type CellularProcess - { - id: String! - label: String - } - -type ChemicalExposure - { - id: String! - label: String - } - -type ChemicalExposureToGenePredicate - { - id: String! - label: String - } - -interface CompoundExpression - { - } - -type Disease - { - id: String! - label: String - } - -type DiseaseCellularProcessRelationship - { - qualifier: String - subject: Disease - predicate: DiseaseToCellularProcessPredicate - object: CellularProcess - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - -type DiseaseToCellularProcessPredicate - { - id: String! - label: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Gene - { - id: String! - label: String - } - -type GeneExposureRelationship - { - qualifier: String - subject: ChemicalExposure - predicate: ChemicalExposureToGenePredicate - object: Gene - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - -type IBDAnnotations - { - genes: [Gene] - exposures: [ChemicalExposure] - geneExposuresRelationships: [GeneExposureRelationship] - diseases: [Disease] - cellularProcess: [CellularProcess] - diseaseCellularProcessRelationships: [DiseaseCellularProcessRelationship] - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/ibd_literature/ibd_literature.py b/projects/ibd_literature/ibd_literature.py deleted file mode 100644 index 29ee09d90..000000000 --- a/projects/ibd_literature/ibd_literature.py +++ /dev/null @@ -1,673 +0,0 @@ -# Auto generated from ibd_literature.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T11:00:44 -# Schema: ibd-literature-template -# -# id: http://w3id.org/ontogpt/ibd_literature -# description: A template for extracting information from IBD literature -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CHEBI = CurieNamespace('CHEBI', 'http://purl.obolibrary.org/obo/CHEBI_') -ECTO = CurieNamespace('ECTO', 'http://purl.obolibrary.org/obo/ECTO_') -EXO = CurieNamespace('ExO', 'http://purl.obolibrary.org/obo/ExO_') -GO = CurieNamespace('GO', 'http://example.org/UNKNOWN/GO/') -HGNC = CurieNamespace('HGNC', 'http://identifiers.org/hgnc/') -MONDO = CurieNamespace('MONDO', 'http://example.org/UNKNOWN/MONDO/') -NCIT = CurieNamespace('NCIT', 'http://purl.obolibrary.org/obo/NCIT_') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -IBDLIT = CurieNamespace('ibdlit', 'http://w3id.org/ontogpt/ibd_literature/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = IBDLIT - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class GeneId(NamedEntityId): - pass - - -class DiseaseId(NamedEntityId): - pass - - -class CellularProcessId(NamedEntityId): - pass - - -class ChemicalExposureId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -class DiseaseToCellularProcessPredicateId(RelationshipTypeId): - pass - - -class ChemicalExposureToGenePredicateId(RelationshipTypeId): - pass - - -@dataclass -class IBDAnnotations(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.IBDAnnotations - class_class_curie: ClassVar[str] = "ibdlit:IBDAnnotations" - class_name: ClassVar[str] = "IBDAnnotations" - class_model_uri: ClassVar[URIRef] = IBDLIT.IBDAnnotations - - genes: Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]] = empty_list() - exposures: Optional[Union[Union[str, ChemicalExposureId], List[Union[str, ChemicalExposureId]]]] = empty_list() - gene_exposures_relationships: Optional[Union[Union[dict, "GeneExposureRelationship"], List[Union[dict, "GeneExposureRelationship"]]]] = empty_list() - diseases: Optional[Union[Union[str, DiseaseId], List[Union[str, DiseaseId]]]] = empty_list() - cellular_process: Optional[Union[Union[str, CellularProcessId], List[Union[str, CellularProcessId]]]] = empty_list() - disease_cellular_process_relationships: Optional[Union[Union[dict, "DiseaseCellularProcessRelationship"], List[Union[dict, "DiseaseCellularProcessRelationship"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.genes, list): - self.genes = [self.genes] if self.genes is not None else [] - self.genes = [v if isinstance(v, GeneId) else GeneId(v) for v in self.genes] - - if not isinstance(self.exposures, list): - self.exposures = [self.exposures] if self.exposures is not None else [] - self.exposures = [v if isinstance(v, ChemicalExposureId) else ChemicalExposureId(v) for v in self.exposures] - - if not isinstance(self.gene_exposures_relationships, list): - self.gene_exposures_relationships = [self.gene_exposures_relationships] if self.gene_exposures_relationships is not None else [] - self.gene_exposures_relationships = [v if isinstance(v, GeneExposureRelationship) else GeneExposureRelationship(**as_dict(v)) for v in self.gene_exposures_relationships] - - if not isinstance(self.diseases, list): - self.diseases = [self.diseases] if self.diseases is not None else [] - self.diseases = [v if isinstance(v, DiseaseId) else DiseaseId(v) for v in self.diseases] - - if not isinstance(self.cellular_process, list): - self.cellular_process = [self.cellular_process] if self.cellular_process is not None else [] - self.cellular_process = [v if isinstance(v, CellularProcessId) else CellularProcessId(v) for v in self.cellular_process] - - if not isinstance(self.disease_cellular_process_relationships, list): - self.disease_cellular_process_relationships = [self.disease_cellular_process_relationships] if self.disease_cellular_process_relationships is not None else [] - self.disease_cellular_process_relationships = [v if isinstance(v, DiseaseCellularProcessRelationship) else DiseaseCellularProcessRelationship(**as_dict(v)) for v in self.disease_cellular_process_relationships] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = IBDLIT.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = IBDLIT.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.Gene - class_class_curie: ClassVar[str] = "ibdlit:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = IBDLIT.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Disease(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.Disease - class_class_curie: ClassVar[str] = "ibdlit:Disease" - class_name: ClassVar[str] = "Disease" - class_model_uri: ClassVar[URIRef] = IBDLIT.Disease - - id: Union[str, DiseaseId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiseaseId): - self.id = DiseaseId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class CellularProcess(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.CellularProcess - class_class_curie: ClassVar[str] = "ibdlit:CellularProcess" - class_name: ClassVar[str] = "CellularProcess" - class_model_uri: ClassVar[URIRef] = IBDLIT.CellularProcess - - id: Union[str, CellularProcessId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, CellularProcessId): - self.id = CellularProcessId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalExposure(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.ChemicalExposure - class_class_curie: ClassVar[str] = "ibdlit:ChemicalExposure" - class_name: ClassVar[str] = "ChemicalExposure" - class_model_uri: ClassVar[URIRef] = IBDLIT.ChemicalExposure - - id: Union[str, ChemicalExposureId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalExposureId): - self.id = ChemicalExposureId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = IBDLIT.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = IBDLIT.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class DiseaseCellularProcessRelationship(Triple): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.DiseaseCellularProcessRelationship - class_class_curie: ClassVar[str] = "ibdlit:DiseaseCellularProcessRelationship" - class_name: ClassVar[str] = "DiseaseCellularProcessRelationship" - class_model_uri: ClassVar[URIRef] = IBDLIT.DiseaseCellularProcessRelationship - - subject: Optional[Union[str, DiseaseId]] = None - predicate: Optional[Union[str, DiseaseToCellularProcessPredicateId]] = None - object: Optional[Union[str, CellularProcessId]] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, DiseaseId): - self.subject = DiseaseId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, DiseaseToCellularProcessPredicateId): - self.predicate = DiseaseToCellularProcessPredicateId(self.predicate) - - if self.object is not None and not isinstance(self.object, CellularProcessId): - self.object = CellularProcessId(self.object) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class GeneExposureRelationship(Triple): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.GeneExposureRelationship - class_class_curie: ClassVar[str] = "ibdlit:GeneExposureRelationship" - class_name: ClassVar[str] = "GeneExposureRelationship" - class_model_uri: ClassVar[URIRef] = IBDLIT.GeneExposureRelationship - - subject: Optional[Union[str, ChemicalExposureId]] = None - predicate: Optional[Union[str, ChemicalExposureToGenePredicateId]] = None - object: Optional[Union[str, GeneId]] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, ChemicalExposureId): - self.subject = ChemicalExposureId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, ChemicalExposureToGenePredicateId): - self.predicate = ChemicalExposureToGenePredicateId(self.predicate) - - if self.object is not None and not isinstance(self.object, GeneId): - self.object = GeneId(self.object) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = IBDLIT.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = IBDLIT.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class DiseaseToCellularProcessPredicate(RelationshipType): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.DiseaseToCellularProcessPredicate - class_class_curie: ClassVar[str] = "ibdlit:DiseaseToCellularProcessPredicate" - class_name: ClassVar[str] = "DiseaseToCellularProcessPredicate" - class_model_uri: ClassVar[URIRef] = IBDLIT.DiseaseToCellularProcessPredicate - - id: Union[str, DiseaseToCellularProcessPredicateId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiseaseToCellularProcessPredicateId): - self.id = DiseaseToCellularProcessPredicateId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalExposureToGenePredicate(RelationshipType): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = IBDLIT.ChemicalExposureToGenePredicate - class_class_curie: ClassVar[str] = "ibdlit:ChemicalExposureToGenePredicate" - class_name: ClassVar[str] = "ChemicalExposureToGenePredicate" - class_model_uri: ClassVar[URIRef] = IBDLIT.ChemicalExposureToGenePredicate - - id: Union[str, ChemicalExposureToGenePredicateId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalExposureToGenePredicateId): - self.id = ChemicalExposureToGenePredicateId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = IBDLIT.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = IBDLIT.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.iBDAnnotations__genes = Slot(uri=IBDLIT.genes, name="iBDAnnotations__genes", curie=IBDLIT.curie('genes'), - model_uri=IBDLIT.iBDAnnotations__genes, domain=None, range=Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]]) - -slots.iBDAnnotations__exposures = Slot(uri=IBDLIT.exposures, name="iBDAnnotations__exposures", curie=IBDLIT.curie('exposures'), - model_uri=IBDLIT.iBDAnnotations__exposures, domain=None, range=Optional[Union[Union[str, ChemicalExposureId], List[Union[str, ChemicalExposureId]]]]) - -slots.iBDAnnotations__gene_exposures_relationships = Slot(uri=IBDLIT.gene_exposures_relationships, name="iBDAnnotations__gene_exposures_relationships", curie=IBDLIT.curie('gene_exposures_relationships'), - model_uri=IBDLIT.iBDAnnotations__gene_exposures_relationships, domain=None, range=Optional[Union[Union[dict, GeneExposureRelationship], List[Union[dict, GeneExposureRelationship]]]]) - -slots.iBDAnnotations__diseases = Slot(uri=IBDLIT.diseases, name="iBDAnnotations__diseases", curie=IBDLIT.curie('diseases'), - model_uri=IBDLIT.iBDAnnotations__diseases, domain=None, range=Optional[Union[Union[str, DiseaseId], List[Union[str, DiseaseId]]]]) - -slots.iBDAnnotations__cellular_process = Slot(uri=IBDLIT.cellular_process, name="iBDAnnotations__cellular_process", curie=IBDLIT.curie('cellular_process'), - model_uri=IBDLIT.iBDAnnotations__cellular_process, domain=None, range=Optional[Union[Union[str, CellularProcessId], List[Union[str, CellularProcessId]]]]) - -slots.iBDAnnotations__disease_cellular_process_relationships = Slot(uri=IBDLIT.disease_cellular_process_relationships, name="iBDAnnotations__disease_cellular_process_relationships", curie=IBDLIT.curie('disease_cellular_process_relationships'), - model_uri=IBDLIT.iBDAnnotations__disease_cellular_process_relationships, domain=None, range=Optional[Union[Union[dict, DiseaseCellularProcessRelationship], List[Union[dict, DiseaseCellularProcessRelationship]]]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=IBDLIT.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=IBDLIT.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=IBDLIT.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=IBDLIT.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=IBDLIT.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=IBDLIT.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=IBDLIT.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=IBDLIT.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=IBDLIT.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=IBDLIT.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=IBDLIT.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=IBDLIT.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=IBDLIT.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=IBDLIT.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=IBDLIT.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=IBDLIT.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=IBDLIT.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=IBDLIT.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=IBDLIT.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=IBDLIT.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=IBDLIT.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=IBDLIT.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=IBDLIT.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=IBDLIT.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=IBDLIT.annotatorResult__object_text, domain=None, range=Optional[str]) - -slots.DiseaseCellularProcessRelationship_subject = Slot(uri=IBDLIT.subject, name="DiseaseCellularProcessRelationship_subject", curie=IBDLIT.curie('subject'), - model_uri=IBDLIT.DiseaseCellularProcessRelationship_subject, domain=DiseaseCellularProcessRelationship, range=Optional[Union[str, DiseaseId]]) - -slots.DiseaseCellularProcessRelationship_predicate = Slot(uri=IBDLIT.predicate, name="DiseaseCellularProcessRelationship_predicate", curie=IBDLIT.curie('predicate'), - model_uri=IBDLIT.DiseaseCellularProcessRelationship_predicate, domain=DiseaseCellularProcessRelationship, range=Optional[Union[str, DiseaseToCellularProcessPredicateId]]) - -slots.DiseaseCellularProcessRelationship_object = Slot(uri=IBDLIT.object, name="DiseaseCellularProcessRelationship_object", curie=IBDLIT.curie('object'), - model_uri=IBDLIT.DiseaseCellularProcessRelationship_object, domain=DiseaseCellularProcessRelationship, range=Optional[Union[str, CellularProcessId]]) - -slots.DiseaseCellularProcessRelationship_subject_qualifier = Slot(uri=IBDLIT.subject_qualifier, name="DiseaseCellularProcessRelationship_subject_qualifier", curie=IBDLIT.curie('subject_qualifier'), - model_uri=IBDLIT.DiseaseCellularProcessRelationship_subject_qualifier, domain=DiseaseCellularProcessRelationship, range=Optional[Union[str, NamedEntityId]]) - -slots.DiseaseCellularProcessRelationship_object_qualifier = Slot(uri=IBDLIT.object_qualifier, name="DiseaseCellularProcessRelationship_object_qualifier", curie=IBDLIT.curie('object_qualifier'), - model_uri=IBDLIT.DiseaseCellularProcessRelationship_object_qualifier, domain=DiseaseCellularProcessRelationship, range=Optional[Union[str, NamedEntityId]]) - -slots.GeneExposureRelationship_subject = Slot(uri=IBDLIT.subject, name="GeneExposureRelationship_subject", curie=IBDLIT.curie('subject'), - model_uri=IBDLIT.GeneExposureRelationship_subject, domain=GeneExposureRelationship, range=Optional[Union[str, ChemicalExposureId]]) - -slots.GeneExposureRelationship_predicate = Slot(uri=IBDLIT.predicate, name="GeneExposureRelationship_predicate", curie=IBDLIT.curie('predicate'), - model_uri=IBDLIT.GeneExposureRelationship_predicate, domain=GeneExposureRelationship, range=Optional[Union[str, ChemicalExposureToGenePredicateId]]) - -slots.GeneExposureRelationship_object = Slot(uri=IBDLIT.object, name="GeneExposureRelationship_object", curie=IBDLIT.curie('object'), - model_uri=IBDLIT.GeneExposureRelationship_object, domain=GeneExposureRelationship, range=Optional[Union[str, GeneId]]) - -slots.GeneExposureRelationship_subject_qualifier = Slot(uri=IBDLIT.subject_qualifier, name="GeneExposureRelationship_subject_qualifier", curie=IBDLIT.curie('subject_qualifier'), - model_uri=IBDLIT.GeneExposureRelationship_subject_qualifier, domain=GeneExposureRelationship, range=Optional[Union[str, NamedEntityId]]) - -slots.GeneExposureRelationship_object_qualifier = Slot(uri=IBDLIT.object_qualifier, name="GeneExposureRelationship_object_qualifier", curie=IBDLIT.curie('object_qualifier'), - model_uri=IBDLIT.GeneExposureRelationship_object_qualifier, domain=GeneExposureRelationship, range=Optional[Union[str, NamedEntityId]]) \ No newline at end of file diff --git a/projects/ibd_literature/jsonld/ibd_literature.context.jsonld b/projects/ibd_literature/jsonld/ibd_literature.context.jsonld deleted file mode 100644 index 867e19231..000000000 --- a/projects/ibd_literature/jsonld/ibd_literature.context.jsonld +++ /dev/null @@ -1,164 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T11:00:34", - "source": "ibd_literature.yaml" - }, - "@context": { - "CHEBI": { - "@id": "http://purl.obolibrary.org/obo/CHEBI_", - "@prefix": true - }, - "ECTO": { - "@id": "http://purl.obolibrary.org/obo/ECTO_", - "@prefix": true - }, - "ExO": { - "@id": "http://purl.obolibrary.org/obo/ExO_", - "@prefix": true - }, - "GO": "http://example.org/UNKNOWN/GO/", - "HGNC": "http://identifiers.org/hgnc/", - "MONDO": "http://example.org/UNKNOWN/MONDO/", - "NCIT": { - "@id": "http://purl.obolibrary.org/obo/NCIT_", - "@prefix": true - }, - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "ibdlit": "http://w3id.org/ontogpt/ibd_literature/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/ibd_literature/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "cellular_process": { - "@type": "@id" - }, - "disease_cellular_process_relationships": { - "@type": "@id" - }, - "diseases": { - "@type": "@id" - }, - "exposures": { - "@type": "@id" - }, - "gene_exposures_relationships": { - "@type": "@id" - }, - "genes": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/ibd_literature/jsonld/ibd_literature.jsonld b/projects/ibd_literature/jsonld/ibd_literature.jsonld deleted file mode 100644 index 9e613ceab..000000000 --- a/projects/ibd_literature/jsonld/ibd_literature.jsonld +++ /dev/null @@ -1,1529 +0,0 @@ -{ - "name": "ibd-literature-template", - "description": "A template for extracting information from IBD literature", - "title": "IBD Literature Template", - "id": "http://w3id.org/ontogpt/ibd_literature", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "CHEBI", - "prefix_reference": "http://purl.obolibrary.org/obo/CHEBI_" - }, - { - "prefix_prefix": "ECTO", - "prefix_reference": "http://purl.obolibrary.org/obo/ECTO_" - }, - { - "prefix_prefix": "ExO", - "prefix_reference": "http://purl.obolibrary.org/obo/ExO_" - }, - { - "prefix_prefix": "HGNC", - "prefix_reference": "http://identifiers.org/hgnc/" - }, - { - "prefix_prefix": "NCIT", - "prefix_reference": "http://purl.obolibrary.org/obo/NCIT_" - }, - { - "prefix_prefix": "core", - "prefix_reference": "http://w3id.org/ontogpt/core/" - }, - { - "prefix_prefix": "ibdlit", - "prefix_reference": "http://w3id.org/ontogpt/ibd_literature/" - }, - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - } - ], - "default_prefix": "ibdlit", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "iBDAnnotations__genes", - "description": "semicolon-separated list of genes", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/genes", - "multivalued": true, - "alias": "genes", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__exposures", - "annotations": [ - { - "tag": "prompt", - "value": "a chemical or molecule whose direct or indirect effects cause one or more entities to experience biological change", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of exposures", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/exposures", - "multivalued": true, - "alias": "exposures", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "ChemicalExposure", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__gene_exposures_relationships", - "description": "semicolon-separated list of gene to molecular activity relationships", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/gene_exposures_relationships", - "multivalued": true, - "alias": "gene_exposures_relationships", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "GeneExposureRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__diseases", - "description": "semicolon-separated list of diseases", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/diseases", - "multivalued": true, - "alias": "diseases", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "Disease", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__cellular_process", - "description": "semicolon-separated list of cellular processes", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/cellular_process", - "multivalued": true, - "alias": "cellular_process", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "CellularProcess", - "@type": "SlotDefinition" - }, - { - "name": "iBDAnnotations__disease_cellular_process_relationships", - "description": "semicolon-separated list of disease to cellular process relationships", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/disease_cellular_process_relationships", - "multivalued": true, - "alias": "disease_cellular_process_relationships", - "owner": "IBDAnnotations", - "domain_of": [ - "IBDAnnotations" - ], - "range": "DiseaseCellularProcessRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "DiseaseCellularProcessRelationship_subject", - "description": "The name of the disease.", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "triple__subject", - "domain": "DiseaseCellularProcessRelationship", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/subject", - "alias": "subject", - "owner": "DiseaseCellularProcessRelationship", - "domain_of": [ - "DiseaseCellularProcessRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "subject", - "range": "Disease", - "@type": "SlotDefinition" - }, - { - "name": "DiseaseCellularProcessRelationship_predicate", - "description": "The name of the type of relationship between a disease and a cellular process.", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "triple__predicate", - "domain": "DiseaseCellularProcessRelationship", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/predicate", - "alias": "predicate", - "owner": "DiseaseCellularProcessRelationship", - "domain_of": [ - "DiseaseCellularProcessRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "predicate", - "range": "DiseaseToCellularProcessPredicate", - "@type": "SlotDefinition" - }, - { - "name": "DiseaseCellularProcessRelationship_object", - "description": "The name of the cellular process.", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "triple__object", - "domain": "DiseaseCellularProcessRelationship", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/object", - "alias": "object", - "owner": "DiseaseCellularProcessRelationship", - "domain_of": [ - "DiseaseCellularProcessRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "object", - "range": "CellularProcess", - "@type": "SlotDefinition" - }, - { - "name": "DiseaseCellularProcessRelationship_subject_qualifier", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "triple__subject_qualifier", - "domain": "DiseaseCellularProcessRelationship", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/subject_qualifier", - "alias": "subject_qualifier", - "owner": "DiseaseCellularProcessRelationship", - "domain_of": [ - "DiseaseCellularProcessRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "subject_qualifier", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "DiseaseCellularProcessRelationship_object_qualifier", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "triple__object_qualifier", - "domain": "DiseaseCellularProcessRelationship", - "slot_uri": "http://w3id.org/ontogpt/ibd_literature/object_qualifier", - "alias": "object_qualifier", - "owner": "DiseaseCellularProcessRelationship", - "domain_of": [ - "DiseaseCellularProcessRelationship" - ], - "is_usage_slot": true, - "usage_slot_name": "object_qualifier", - "range": "NamedEntity", - 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This comes second in the pair.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ibd_literature/Gene", - "@type": "ClassDefinition" - }, - { - "name": "Disease", - "id_prefixes": [ - "MONDO" - ], - "definition_uri": "http://w3id.org/ontogpt/ibd_literature/Disease", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:mondo", - "@type": "Annotation" - }, - { - "tag": "prompt", - "value": "the name of the disease", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ibd_literature/Disease", - "@type": "ClassDefinition" - }, - { - "name": "CellularProcess", - "id_prefixes": [ - "GO" - ], - "definition_uri": "http://w3id.org/ontogpt/ibd_literature/CellularProcess", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go", - "@type": "Annotation" - }, - { - "tag": "prompt", - "value": "the name of the cellular process", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ibd_literature/CellularProcess", - "@type": "ClassDefinition" - }, - { - "name": "DiseaseToCellularProcessPredicate", - "id_prefixes": [ - "RO" - ], - "definition_uri": "http://w3id.org/ontogpt/ibd_literature/DiseaseToCellularProcessPredicate", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:ro", - "@type": "Annotation" - }, - { - "tag": "prompt", - "value": "the name of the type of relationship between a disease and a cellular process.", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "RelationshipType", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ibd_literature/DiseaseToCellularProcessPredicate", - "@type": "ClassDefinition" - }, - { - "name": "DiseaseCellularProcessRelationship", - "definition_uri": "http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "Triple", - "slots": [ - "triple__qualifier", - "DiseaseCellularProcessRelationship_subject", - "DiseaseCellularProcessRelationship_predicate", - "DiseaseCellularProcessRelationship_object", - "DiseaseCellularProcessRelationship_subject_qualifier", - "DiseaseCellularProcessRelationship_object_qualifier" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship", - "@type": "ClassDefinition" - }, - { - "name": "ChemicalExposure", - "id_prefixes": [ - "CHEBI", - "ECTO", - "ExO", - "NCIT" - ], - "definition_uri": "http://w3id.org/ontogpt/ibd_literature/ChemicalExposure", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:ecto, sqlite:obo:chebi", - "@type": "Annotation" - }, - { - "tag": "prompt", - "value": "the name of the exposure, such as a exposure to a chemical toxin. 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"@type": "ClassDefinition" - }, - { - "name": "GeneExposureRelationship", - "definition_uri": "http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship", - "from_schema": "http://w3id.org/ontogpt/ibd_literature", - "is_a": "Triple", - "slots": [ - "triple__qualifier", - "GeneExposureRelationship_subject", - "GeneExposureRelationship_predicate", - "GeneExposureRelationship_object", - "GeneExposureRelationship_subject_qualifier", - "GeneExposureRelationship_object_qualifier" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - 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"type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "DiseaseToCellularProcessPredicate", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Gene": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Gene", - "type": "object" - }, - "GeneExposureRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "object": { - "description": "The name of the gene in the pair. This comes second in the pair.", - "type": "string" - }, - "object_qualifier": { - "description": "An optional qualifier or modifier for the gene.", - "type": "string" - }, - "predicate": { - "description": "The name of the type of relationship between a chemical exposure and a gene.", - "type": "string" - }, - "qualifier": { - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "type": "string" - }, - "subject": { - "description": "The name of the exposure, such as a exposure to a chemical toxin.", - "type": "string" - }, - "subject_qualifier": { - "description": "An optional qualifier or modifier for the chemical exposure.", - "type": "string" - } - }, - "title": "GeneExposureRelationship", - "type": "object" - }, - "IBDAnnotations": { - "additionalProperties": false, - "description": "", - "properties": { - "cellular_process": { - "description": "semicolon-separated list of cellular processes", - "items": { - "type": "string" - }, - "type": "array" - }, - "disease_cellular_process_relationships": { - "description": "semicolon-separated list of disease to cellular process relationships", - "items": { - "$ref": "#/$defs/DiseaseCellularProcessRelationship" - }, - "type": "array" - }, - "diseases": { - "description": "semicolon-separated list of diseases", - "items": { - "type": "string" - }, - "type": "array" - }, - "exposures": { - "description": "semicolon-separated list of exposures", - "items": { - "type": "string" - }, - "type": "array" - }, - "gene_exposures_relationships": { - "description": "semicolon-separated list of gene to molecular activity relationships", - "items": { - "$ref": "#/$defs/GeneExposureRelationship" - }, - "type": "array" - }, - "genes": { - "description": "semicolon-separated list of genes", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "IBDAnnotations", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/ibd_literature", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "cellular_process": { - "description": "semicolon-separated list of cellular processes", - "items": { - "type": "string" - }, - "type": "array" - }, - "disease_cellular_process_relationships": { - "description": "semicolon-separated list of disease to cellular process relationships", - "items": { - "$ref": "#/$defs/DiseaseCellularProcessRelationship" - }, - "type": "array" - }, - "diseases": { - "description": "semicolon-separated list of diseases", - "items": { - "type": "string" - }, - "type": "array" - }, - "exposures": { - "description": "semicolon-separated list of exposures", - "items": { - "type": "string" - }, - "type": "array" - }, - "gene_exposures_relationships": { - "description": "semicolon-separated list of gene to molecular activity relationships", - "items": { - "$ref": "#/$defs/GeneExposureRelationship" - }, - "type": "array" - }, - "genes": { - "description": "semicolon-separated list of genes", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "ibd-literature-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/ibd_literature/owl/ibd_literature.owl.ttl b/projects/ibd_literature/owl/ibd_literature.owl.ttl deleted file mode 100644 index 18d2c640e..000000000 --- a/projects/ibd_literature/owl/ibd_literature.owl.ttl +++ /dev/null @@ -1,580 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix NCIT: <http://purl.obolibrary.org/obo/NCIT_> . -@prefix core: <http://w3id.org/ontogpt/core/> . -@prefix ibdlit: <http://w3id.org/ontogpt/ibd_literature/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/ibd_literature> a owl:Ontology ; - rdfs:label "ibd-literature-template" ; - IAO:0000700 core:AnnotatorResult, - core:Any, - core:CompoundExpression, - core:ExtractionResult, - core:NamedEntity, - core:Publication, - core:TextWithTriples, - ibdlit:IBDAnnotations ; - linkml:classes "{'IBDAnnotations': ClassDefinition(name='IBDAnnotations', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ibd_literature/IBDAnnotations', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['iBDAnnotations__genes', 'iBDAnnotations__exposures', 'iBDAnnotations__gene_exposures_relationships', 'iBDAnnotations__diseases', 'iBDAnnotations__cellular_process', 'iBDAnnotations__disease_cellular_process_relationships'], slot_usage={}, attributes={'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'exposures': SlotDefinition(name='exposures', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a chemical or molecule whose direct or indirect effects cause one or more entities to experience biological change', extensions={}, annotations={})}, description='semicolon-separated list of exposures', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalExposure', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_exposures_relationships': SlotDefinition(name='gene_exposures_relationships', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to molecular activity relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneExposureRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'diseases': SlotDefinition(name='diseases', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of diseases', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'cellular_process': SlotDefinition(name='cellular_process', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of cellular processes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CellularProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'disease_cellular_process_relationships': SlotDefinition(name='disease_cellular_process_relationships', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of disease to cellular process relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DiseaseCellularProcessRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='ibdlit:IBDAnnotations', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC'], definition_uri='http://w3id.org/ontogpt/ibd_literature/Gene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hgnc, sqlite:obo:pr', extensions={}, annotations={}), 'prompt': Annotation(tag='prompt', value='the name of the gene in the pair. This comes second in the pair.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='ibdlit:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Disease': ClassDefinition(name='Disease', id_prefixes=['MONDO'], definition_uri='http://w3id.org/ontogpt/ibd_literature/Disease', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:mondo', extensions={}, annotations={}), 'prompt': Annotation(tag='prompt', value='the name of the disease', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='ibdlit:Disease', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CellularProcess': ClassDefinition(name='CellularProcess', id_prefixes=['GO'], definition_uri='http://w3id.org/ontogpt/ibd_literature/CellularProcess', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={}), 'prompt': Annotation(tag='prompt', value='the name of the cellular process', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='ibdlit:CellularProcess', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'DiseaseToCellularProcessPredicate': ClassDefinition(name='DiseaseToCellularProcessPredicate', id_prefixes=['RO'], definition_uri='http://w3id.org/ontogpt/ibd_literature/DiseaseToCellularProcessPredicate', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:ro', extensions={}, annotations={}), 'prompt': Annotation(tag='prompt', value='the name of the type of relationship between a disease and a cellular process.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='RelationshipType', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='ibdlit:DiseaseToCellularProcessPredicate', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'DiseaseCellularProcessRelationship': ClassDefinition(name='DiseaseCellularProcessRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ibd_literature/DiseaseCellularProcessRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='Triple', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__qualifier', 'DiseaseCellularProcessRelationship_subject', 'DiseaseCellularProcessRelationship_predicate', 'DiseaseCellularProcessRelationship_object', 'DiseaseCellularProcessRelationship_subject_qualifier', 'DiseaseCellularProcessRelationship_object_qualifier'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The name of the disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The name of the type of relationship between a disease and a cellular process.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__predicate', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DiseaseToCellularProcessPredicate', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The name of the cellular process.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CellularProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='ibdlit:DiseaseCellularProcessRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ChemicalExposure': ClassDefinition(name='ChemicalExposure', id_prefixes=['CHEBI', 'ECTO', 'ExO', 'NCIT'], definition_uri='http://w3id.org/ontogpt/ibd_literature/ChemicalExposure', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:ecto, sqlite:obo:chebi', extensions={}, annotations={}), 'prompt': Annotation(tag='prompt', value='the name of the exposure, such as a exposure to a chemical toxin. For example, CHEBI:17968 butyrate.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='ibdlit:ChemicalExposure', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ChemicalExposureToGenePredicate': ClassDefinition(name='ChemicalExposureToGenePredicate', id_prefixes=['RO'], definition_uri='http://w3id.org/ontogpt/ibd_literature/ChemicalExposureToGenePredicate', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:ro', extensions={}, annotations={}), 'prompt': Annotation(tag='prompt', value='the name of the type of relationship between a chemical exposure and a gene.', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='RelationshipType', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='ibdlit:ChemicalExposureToGenePredicate', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneExposureRelationship': ClassDefinition(name='GeneExposureRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ibd_literature/GeneExposureRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/ibd_literature', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='Triple', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__qualifier', 'GeneExposureRelationship_subject', 'GeneExposureRelationship_predicate', 'GeneExposureRelationship_object', 'GeneExposureRelationship_subject_qualifier', 'GeneExposureRelationship_object_qualifier'], slot_usage={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The name of the exposure, such as a exposure to a chemical toxin.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalExposure', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The name of the type of relationship between a chemical exposure and a gene.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__predicate', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalExposureToGenePredicate', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The name of the gene in the pair. This comes second in the pair.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the chemical exposure.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__subject_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the gene.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='triple__object_qualifier', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='ibdlit:GeneExposureRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/ibd_literature" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -core:AnnotatorResult a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:object_id ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:object_text ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:subject_text ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -core:ExtractionResult a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:Any ; - owl:onProperty core:extracted_object ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:raw_completion_output ], - [ a owl:Restriction ; - owl:allValuesFrom core:Any ; - owl:onProperty core:named_entities ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:input_title ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:prompt ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:input_text ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:input_id ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -core:TextWithTriples a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:Publication ; - owl:onProperty core:publication ], - [ a owl:Restriction ; - owl:allValuesFrom core:Triple ; - owl:onProperty core:triples ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -core:abstract a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -core:combined_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -core:extracted_object a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range core:Any ; - skos:definition "The complex objects extracted from the text" . - -core:full_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -core:input_id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -core:input_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -core:input_title a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -core:named_entities a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range core:Any ; - skos:definition "Named entities extracted from the text" . - -core:object_id a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -core:object_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -core:prompt a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -core:publication a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - ibdlit:prompt.skip "true" ; - rdfs:range core:Publication . - -core:qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -core:raw_completion_output a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -core:subject_text a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -core:title a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -core:triples a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range core:Triple . - -ibdlit:IBDAnnotations a owl:Class, - linkml:ClassDefinition ; - rdfs:label "IBDAnnotations" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ibdlit:ChemicalExposure ; - owl:onProperty ibdlit:exposures ], - [ a owl:Restriction ; - owl:allValuesFrom ibdlit:CellularProcess ; - owl:onProperty ibdlit:cellular_process ], - [ a owl:Restriction ; - owl:allValuesFrom ibdlit:DiseaseCellularProcessRelationship ; - owl:onProperty ibdlit:disease_cellular_process_relationships ], - [ a owl:Restriction ; - owl:allValuesFrom ibdlit:Disease ; - owl:onProperty ibdlit:diseases ], - [ a owl:Restriction ; - owl:allValuesFrom ibdlit:Gene ; - owl:onProperty ibdlit:genes ], - [ a owl:Restriction ; - owl:allValuesFrom ibdlit:GeneExposureRelationship ; - owl:onProperty ibdlit:gene_exposures_relationships ] ; - linkml:attributes "{'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of genes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'exposures': SlotDefinition(name='exposures', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a chemical or molecule whose direct or indirect effects cause one or more entities to experience biological change', extensions={}, annotations={})}, description='semicolon-separated list of exposures', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalExposure', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_exposures_relationships': SlotDefinition(name='gene_exposures_relationships', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of gene to molecular activity relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneExposureRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'diseases': SlotDefinition(name='diseases', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of diseases', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'cellular_process': SlotDefinition(name='cellular_process', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of cellular processes', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CellularProcess', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'disease_cellular_process_relationships': SlotDefinition(name='disease_cellular_process_relationships', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of disease to cellular process relationships', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DiseaseCellularProcessRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -ibdlit:cellular_process a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "cellular_process" ; - rdfs:range ibdlit:CellularProcess ; - skos:definition "semicolon-separated list of cellular processes" . - -ibdlit:disease_cellular_process_relationships a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "disease_cellular_process_relationships" ; - rdfs:range ibdlit:DiseaseCellularProcessRelationship ; - skos:definition "semicolon-separated list of disease to cellular process relationships" . - -ibdlit:diseases a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "diseases" ; - rdfs:range ibdlit:Disease ; - skos:definition "semicolon-separated list of diseases" . - -ibdlit:exposures a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "exposures" ; - ibdlit:prompt "a chemical or molecule whose direct or indirect effects cause one or more entities to experience biological change" ; - rdfs:range ibdlit:ChemicalExposure ; - skos:definition "semicolon-separated list of exposures" . - -ibdlit:gene_exposures_relationships a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_exposures_relationships" ; - rdfs:range ibdlit:GeneExposureRelationship ; - skos:definition "semicolon-separated list of gene to molecular activity relationships" . - -ibdlit:genes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "genes" ; - rdfs:range ibdlit:Gene ; - skos:definition "semicolon-separated list of genes" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - ibdlit:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -NCIT:C149701 a core:NullDataOptions, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -NCIT:C18902 a core:NullDataOptions, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -core:CompoundExpression a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a core:NullDataOptions, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -core:id a owl:ObjectProperty, - linkml:SlotDefinition . - -core:object a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range core:NamedEntity . - -core:object_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range core:NamedEntity ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -core:predicate a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range core:RelationshipType . - -core:subject a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range core:NamedEntity . - -core:subject_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range core:NamedEntity ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -ibdlit:ChemicalExposureToGenePredicate a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalExposureToGenePredicate" ; - ibdlit:annotators "sqlite:obo:ro" ; - ibdlit:prompt "the name of the type of relationship between a chemical exposure and a gene." ; - rdfs:subClassOf core:RelationshipType ; - linkml:attributes "{}" ; - linkml:is_a "RelationshipType" . - -ibdlit:DiseaseToCellularProcessPredicate a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DiseaseToCellularProcessPredicate" ; - ibdlit:annotators "sqlite:obo:ro" ; - ibdlit:prompt "the name of the type of relationship between a disease and a cellular process." ; - rdfs:subClassOf core:RelationshipType ; - linkml:attributes "{}" ; - linkml:is_a "RelationshipType" . - -ibdlit:object a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:domain ibdlit:DiseaseCellularProcessRelationship, - ibdlit:GeneExposureRelationship ; - rdfs:range ibdlit:CellularProcess, - ibdlit:Gene ; - rdfs:subPropertyOf core:object ; - skos:definition "The name of the cellular process.", - "The name of the gene in the pair. This comes second in the pair." ; - linkml:is_a "triple__object" . - -ibdlit:object_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:domain ibdlit:DiseaseCellularProcessRelationship, - ibdlit:GeneExposureRelationship ; - rdfs:range core:NamedEntity ; - rdfs:subPropertyOf core:object_qualifier ; - skos:definition "An optional qualifier or modifier for the gene." ; - linkml:is_a "triple__object_qualifier" . - -ibdlit:predicate a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:domain ibdlit:DiseaseCellularProcessRelationship, - ibdlit:GeneExposureRelationship ; - rdfs:range ibdlit:ChemicalExposureToGenePredicate, - ibdlit:DiseaseToCellularProcessPredicate ; - rdfs:subPropertyOf core:predicate ; - skos:definition "The name of the type of relationship between a chemical exposure and a gene.", - "The name of the type of relationship between a disease and a cellular process." ; - linkml:is_a "triple__predicate" . - -ibdlit:subject a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:domain ibdlit:DiseaseCellularProcessRelationship, - ibdlit:GeneExposureRelationship ; - rdfs:range ibdlit:ChemicalExposure, - ibdlit:Disease ; - rdfs:subPropertyOf core:subject ; - skos:definition "The name of the disease.", - "The name of the exposure, such as a exposure to a chemical toxin." ; - linkml:is_a "triple__subject" . - -ibdlit:subject_qualifier a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:domain ibdlit:DiseaseCellularProcessRelationship, - ibdlit:GeneExposureRelationship ; - rdfs:range core:NamedEntity ; - rdfs:subPropertyOf core:subject_qualifier ; - skos:definition "An optional qualifier or modifier for the chemical exposure." ; - linkml:is_a "triple__subject_qualifier" . - -core:NullDataOptions a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( NCIT:C149701 NCIT:C18902 <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values NCIT:C149701, - NCIT:C18902, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -core:Publication a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:title ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:abstract ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:full_text ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:id ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:combined_text ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -core:RelationshipType a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf core:NamedEntity ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -core:Triple a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty core:object_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty core:subject ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty core:subject_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty core:qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty core:object ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:RelationshipType ; - owl:onProperty core:predicate ], - core:CompoundExpression ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -ibdlit:CellularProcess a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CellularProcess" ; - ibdlit:annotators "sqlite:obo:go" ; - ibdlit:prompt "the name of the cellular process" ; - rdfs:subClassOf core:NamedEntity ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -ibdlit:ChemicalExposure a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalExposure" ; - ibdlit:annotators "sqlite:obo:ecto, sqlite:obo:chebi" ; - ibdlit:prompt "the name of the exposure, such as a exposure to a chemical toxin. For example, CHEBI:17968 butyrate." ; - rdfs:subClassOf core:NamedEntity ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -ibdlit:Disease a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Disease" ; - ibdlit:annotators "sqlite:obo:mondo" ; - ibdlit:prompt "the name of the disease" ; - rdfs:subClassOf core:NamedEntity ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -ibdlit:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - ibdlit:annotators "sqlite:obo:hgnc, sqlite:obo:pr" ; - ibdlit:prompt "the name of the gene in the pair. This comes second in the pair." ; - rdfs:subClassOf core:NamedEntity ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -core:Any a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -ibdlit:DiseaseCellularProcessRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DiseaseCellularProcessRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ibdlit:DiseaseToCellularProcessPredicate ; - owl:onProperty ibdlit:predicate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty ibdlit:object_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ibdlit:CellularProcess ; - owl:onProperty ibdlit:object ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ibdlit:Disease ; - owl:onProperty ibdlit:subject ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty ibdlit:subject_qualifier ], - core:Triple ; - linkml:attributes "{}" ; - linkml:is_a "Triple" . - -ibdlit:GeneExposureRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneExposureRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ibdlit:Gene ; - owl:onProperty ibdlit:object ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ibdlit:ChemicalExposureToGenePredicate ; - owl:onProperty ibdlit:predicate ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ibdlit:ChemicalExposure ; - owl:onProperty ibdlit:subject ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty ibdlit:object_qualifier ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass core:NamedEntity ; - owl:onProperty ibdlit:subject_qualifier ], - core:Triple ; - linkml:attributes "{}" ; - linkml:is_a "Triple" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -core:NamedEntity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty core:id ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/ibd_literature/prefixmap/ibd_literature.yaml b/projects/ibd_literature/prefixmap/ibd_literature.yaml deleted file mode 100644 index c03580296..000000000 --- a/projects/ibd_literature/prefixmap/ibd_literature.yaml +++ /dev/null @@ -1,42 +0,0 @@ -{ - "CHEBI": "http://purl.obolibrary.org/obo/CHEBI_", - "ECTO": "http://purl.obolibrary.org/obo/ECTO_", - "ExO": "http://purl.obolibrary.org/obo/ExO_", - "GO": "http://example.org/UNKNOWN/GO/", - "HGNC": "http://identifiers.org/hgnc/", - "MONDO": "http://example.org/UNKNOWN/MONDO/", - "NCIT": "http://purl.obolibrary.org/obo/NCIT_", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "ibdlit": "http://w3id.org/ontogpt/ibd_literature/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/ibd_literature/protobuf/ibd_literature.proto b/projects/ibd_literature/protobuf/ibd_literature.proto deleted file mode 100644 index 5addfe224..000000000 --- a/projects/ibd_literature/protobuf/ibd_literature.proto +++ /dev/null @@ -1,92 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message CellularProcess - { - string id = 0 - string label = 0 - } -message ChemicalExposure - { - string id = 0 - string label = 0 - } -message ChemicalExposureToGenePredicate - { - string id = 0 - string label = 0 - } -message Disease - { - string id = 0 - string label = 0 - } -message DiseaseCellularProcessRelationship - { - string qualifier = 0 - disease subject = 0 - diseaseToCellularProcessPredicate predicate = 0 - cellularProcess object = 0 - namedEntity subjectQualifier = 0 - namedEntity objectQualifier = 0 - } -message DiseaseToCellularProcessPredicate - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -message GeneExposureRelationship - { - string qualifier = 0 - chemicalExposure subject = 0 - chemicalExposureToGenePredicate predicate = 0 - gene object = 0 - namedEntity subjectQualifier = 0 - namedEntity objectQualifier = 0 - } -message IBDAnnotations - { - repeated gene genes = 0 - repeated chemicalExposure exposures = 0 - repeated geneExposureRelationship geneExposuresRelationships = 0 - repeated disease diseases = 0 - repeated cellularProcess cellularProcess = 0 - repeated diseaseCellularProcessRelationship diseaseCellularProcessRelationships = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/ibd_literature/shacl/ibd_literature.shacl.ttl b/projects/ibd_literature/shacl/ibd_literature.shacl.ttl deleted file mode 100644 index 6d8d65e79..000000000 --- a/projects/ibd_literature/shacl/ibd_literature.shacl.ttl +++ /dev/null @@ -1,362 +0,0 @@ -@prefix core: <http://w3id.org/ontogpt/core/> . -@prefix ibdlit: <http://w3id.org/ontogpt/ibd_literature/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -core:AnnotatorResult a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path core:subject_text ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path core:object_id ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path core:object_text ] ; - sh:targetClass core:AnnotatorResult . - -core:CompoundExpression a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass core:CompoundExpression . - -core:ExtractionResult a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path core:extracted_object ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path core:input_id ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path core:input_text ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path core:raw_completion_output ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path core:prompt ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path core:input_title ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path core:named_entities ] ; - sh:targetClass core:ExtractionResult . - -core:TextWithTriples a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class core:Triple ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path core:triples ], - [ sh:class core:Publication ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path core:publication ] ; - sh:targetClass core:TextWithTriples . - -ibdlit:IBDAnnotations a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ibdlit:GeneExposureRelationship ; - sh:description "semicolon-separated list of gene to molecular activity relationships" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path ibdlit:gene_exposures_relationships ], - [ sh:class ibdlit:Gene ; - sh:description "semicolon-separated list of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path ibdlit:genes ], - [ sh:class ibdlit:Disease ; - sh:description "semicolon-separated list of diseases" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path ibdlit:diseases ], - [ sh:class ibdlit:ChemicalExposure ; - sh:description "semicolon-separated list of exposures" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path ibdlit:exposures ], - [ sh:class ibdlit:DiseaseCellularProcessRelationship ; - sh:description "semicolon-separated list of disease to cellular process relationships" ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path ibdlit:disease_cellular_process_relationships ], - [ sh:class ibdlit:CellularProcess ; - sh:description "semicolon-separated list of cellular processes" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path ibdlit:cellular_process ] ; - sh:targetClass ibdlit:IBDAnnotations . - -core:Publication a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 3 ; - sh:path core:combined_text ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path core:id ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path core:title ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path core:abstract ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path core:full_text ] ; - sh:targetClass core:Publication . - -core:RelationshipType a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path core:id ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass core:RelationshipType . - -core:Triple a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class core:NamedEntity ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path core:subject_qualifier ], - [ sh:class core:NamedEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path core:subject ], - [ sh:class core:NamedEntity ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path core:object_qualifier ], - [ sh:class core:NamedEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path core:object ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path core:qualifier ], - [ sh:class core:RelationshipType ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path core:predicate ] ; - sh:targetClass core:Triple . - -ibdlit:ChemicalExposureToGenePredicate a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path core:id ] ; - sh:targetClass ibdlit:ChemicalExposureToGenePredicate . - -ibdlit:DiseaseCellularProcessRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ibdlit:DiseaseToCellularProcessPredicate ; - sh:description "The name of the type of relationship between a disease and a cellular process." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path core:predicate ], - [ sh:class core:NamedEntity ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path core:subject_qualifier ], - [ sh:class core:NamedEntity ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path core:object_qualifier ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path core:qualifier ], - [ sh:class ibdlit:Disease ; - sh:description "The name of the disease." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path core:subject ], - [ sh:class ibdlit:CellularProcess ; - sh:description "The name of the cellular process." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path core:object ] ; - sh:targetClass ibdlit:DiseaseCellularProcessRelationship . - -ibdlit:DiseaseToCellularProcessPredicate a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path core:id ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass ibdlit:DiseaseToCellularProcessPredicate . - -ibdlit:GeneExposureRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class ibdlit:Gene ; - sh:description "The name of the gene in the pair. This comes second in the pair." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path core:object ], - [ sh:class ibdlit:ChemicalExposureToGenePredicate ; - sh:description "The name of the type of relationship between a chemical exposure and a gene." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path core:predicate ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path core:qualifier ], - [ sh:class core:NamedEntity ; - sh:description "An optional qualifier or modifier for the gene." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path core:object_qualifier ], - [ sh:class ibdlit:ChemicalExposure ; - sh:description "The name of the exposure, such as a exposure to a chemical toxin." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path core:subject ], - [ sh:class core:NamedEntity ; - sh:description "An optional qualifier or modifier for the chemical exposure." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path core:subject_qualifier ] ; - sh:targetClass ibdlit:GeneExposureRelationship . - -ibdlit:CellularProcess a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path core:id ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass ibdlit:CellularProcess . - -ibdlit:ChemicalExposure a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path core:id ] ; - sh:targetClass ibdlit:ChemicalExposure . - -ibdlit:Disease a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path core:id ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass ibdlit:Disease . - -ibdlit:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path core:id ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass ibdlit:Gene . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -core:NamedEntity a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path core:id ] ; - sh:targetClass core:NamedEntity . - diff --git a/projects/ibd_literature/shex/ibd_literature.shex b/projects/ibd_literature/shex/ibd_literature.shex deleted file mode 100644 index 49662bcc2..000000000 --- a/projects/ibd_literature/shex/ibd_literature.shex +++ /dev/null @@ -1,226 +0,0 @@ -BASE <http://w3id.org/ontogpt/ibd_literature/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<CellularProcess> CLOSED { - ( $<CellularProcess_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <CellularProcess> ] - ) -} - -<ChemicalExposure> CLOSED { - ( $<ChemicalExposure_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <ChemicalExposure> ] - ) -} - -<ChemicalExposureToGenePredicate> CLOSED { - ( $<ChemicalExposureToGenePredicate_tes> ( &core:RelationshipType_tes ; - rdf:type [ core:RelationshipType ] ? - ) ; - rdf:type [ <ChemicalExposureToGenePredicate> ] - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -<Disease> CLOSED { - ( $<Disease_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Disease> ] - ) -} - -<DiseaseCellularProcessRelationship> CLOSED { - ( $<DiseaseCellularProcessRelationship_tes> ( &core:Triple_tes ; - rdf:type [ core:Triple ] ? ; - <subject> @<Disease> ? ; - <predicate> @<DiseaseToCellularProcessPredicate> ? ; - <object> @<CellularProcess> ? ; - <subject_qualifier> @core:NamedEntity ? ; - <object_qualifier> @core:NamedEntity ? - ) ; - rdf:type [ <DiseaseCellularProcessRelationship> ] ? - ) -} - -<DiseaseToCellularProcessPredicate> CLOSED { - ( $<DiseaseToCellularProcessPredicate_tes> ( &core:RelationshipType_tes ; - rdf:type [ core:RelationshipType ] ? - ) ; - rdf:type [ <DiseaseToCellularProcessPredicate> ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<Gene> CLOSED { - ( $<Gene_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Gene> ] - ) -} - -<GeneExposureRelationship> CLOSED { - ( $<GeneExposureRelationship_tes> ( &core:Triple_tes ; - rdf:type [ core:Triple ] ? ; - <subject> @<ChemicalExposure> ? ; - <predicate> @<ChemicalExposureToGenePredicate> ? ; - <object> @<Gene> ? ; - <subject_qualifier> @core:NamedEntity ? ; - <object_qualifier> @core:NamedEntity ? - ) ; - rdf:type [ <GeneExposureRelationship> ] ? - ) -} - -<IBDAnnotations> CLOSED { - ( $<IBDAnnotations_tes> ( <genes> @<Gene> * ; - <exposures> @<ChemicalExposure> * ; - <gene_exposures_relationships> @<GeneExposureRelationship> * ; - <diseases> @<Disease> * ; - <cellular_process> @<CellularProcess> * ; - <disease_cellular_process_relationships> @<DiseaseCellularProcessRelationship> * - ) ; - rdf:type [ <IBDAnnotations> ] ? - ) -} - -core:NamedEntity ( - @<CellularProcess> OR @<ChemicalExposure> OR @<Disease> OR @<Gene> OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType ( - CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) - } OR @<ChemicalExposureToGenePredicate> OR @<DiseaseToCellularProcessPredicate> -) - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple ( - @<DiseaseCellularProcessRelationship> OR @<GeneExposureRelationship> -) - -core:Triple_struct { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/ibd_literature/sqlschema/ibd_literature.sql b/projects/ibd_literature/sqlschema/ibd_literature.sql deleted file mode 100644 index 4d8e2aff9..000000000 --- a/projects/ibd_literature/sqlschema/ibd_literature.sql +++ /dev/null @@ -1,112 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "CellularProcess" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ChemicalExposure" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ChemicalExposureToGenePredicate" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Disease" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "DiseaseToCellularProcessPredicate" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "IBDAnnotations" ( - genes TEXT, - exposures TEXT, - gene_exposures_relationships TEXT, - diseases TEXT, - cellular_process TEXT, - disease_cellular_process_relationships TEXT, - PRIMARY KEY (genes, exposures, gene_exposures_relationships, diseases, cellular_process, disease_cellular_process_relationships) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "DiseaseCellularProcessRelationship" ( - qualifier TEXT, - subject TEXT, - predicate TEXT, - object TEXT, - subject_qualifier TEXT, - object_qualifier TEXT, - PRIMARY KEY (qualifier, subject, predicate, object, subject_qualifier, object_qualifier), - FOREIGN KEY(subject) REFERENCES "Disease" (id), - FOREIGN KEY(predicate) REFERENCES "DiseaseToCellularProcessPredicate" (id), - FOREIGN KEY(object) REFERENCES "CellularProcess" (id) -); - -CREATE TABLE "GeneExposureRelationship" ( - qualifier TEXT, - subject TEXT, - predicate TEXT, - object TEXT, - subject_qualifier TEXT, - object_qualifier TEXT, - PRIMARY KEY (qualifier, subject, predicate, object, subject_qualifier, object_qualifier), - FOREIGN KEY(subject) REFERENCES "ChemicalExposure" (id), - FOREIGN KEY(predicate) REFERENCES "ChemicalExposureToGenePredicate" (id), - FOREIGN KEY(object) REFERENCES "Gene" (id) -); diff --git a/projects/mendelian_disease/docs/AnnotatorResult.md b/projects/mendelian_disease/docs/AnnotatorResult.md deleted file mode 100644 index ba2647512..000000000 --- a/projects/mendelian_disease/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [mendelian_disease:AnnotatorResult](http://w3id.org/ontogpt/mendelian_disease/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/Any.md b/projects/mendelian_disease/docs/Any.md deleted file mode 100644 index a944133e1..000000000 --- a/projects/mendelian_disease/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [mendelian_disease:Any](http://w3id.org/ontogpt/mendelian_disease/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/mendelian_disease/docs/CompoundExpression.md b/projects/mendelian_disease/docs/CompoundExpression.md deleted file mode 100644 index 02d0ad18b..000000000 --- a/projects/mendelian_disease/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [mendelian_disease:CompoundExpression](http://w3id.org/ontogpt/mendelian_disease/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/mendelian_disease/docs/DiseaseCategory.md b/projects/mendelian_disease/docs/DiseaseCategory.md deleted file mode 100644 index 49d9de951..000000000 --- a/projects/mendelian_disease/docs/DiseaseCategory.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: DiseaseCategory - - - - -URI: [mendelian_disease:DiseaseCategory](http://w3id.org/ontogpt/mendelian_disease/DiseaseCategory) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MendelianDisease]-%20subclass_of%200..*>[DiseaseCategory|id(i):string;label(i):string%20%3F],[NamedEntity]^-[DiseaseCategory],[MendelianDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MendelianDisease]-%20subclass_of%200..*>[DiseaseCategory|id(i):string;label(i):string%20%3F],[NamedEntity]^-[DiseaseCategory],[MendelianDisease]) - -## Identifier prefixes - - * MONDO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞subclass_of](mendelianDisease__subclass_of.md)* <sub>0..\*</sub> **[DiseaseCategory](DiseaseCategory.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/ExtractionResult.md b/projects/mendelian_disease/docs/ExtractionResult.md deleted file mode 100644 index 51ffa7131..000000000 --- a/projects/mendelian_disease/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [mendelian_disease:ExtractionResult](http://w3id.org/ontogpt/mendelian_disease/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/mendelian_disease/docs/Gene.md b/projects/mendelian_disease/docs/Gene.md deleted file mode 100644 index 6ce201a82..000000000 --- a/projects/mendelian_disease/docs/Gene.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Gene - - - - -URI: [mendelian_disease:Gene](http://w3id.org/ontogpt/mendelian_disease/Gene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MendelianDisease]-%20genes%200..*>[Gene|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Gene],[MendelianDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MendelianDisease]-%20genes%200..*>[Gene|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Gene],[MendelianDisease]) - -## Identifier prefixes - - * HGNC - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞genes](mendelianDisease__genes.md)* <sub>0..\*</sub> **[Gene](Gene.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/Inheritance.md b/projects/mendelian_disease/docs/Inheritance.md deleted file mode 100644 index a07f579a7..000000000 --- a/projects/mendelian_disease/docs/Inheritance.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Inheritance - - - - -URI: [mendelian_disease:Inheritance](http://w3id.org/ontogpt/mendelian_disease/Inheritance) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MendelianDisease]-%20inheritance%200..1>[Inheritance|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Inheritance],[MendelianDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MendelianDisease]-%20inheritance%200..1>[Inheritance|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Inheritance],[MendelianDisease]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞inheritance](mendelianDisease__inheritance.md)* <sub>0..1</sub> **[Inheritance](Inheritance.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/MendelianDisease.md b/projects/mendelian_disease/docs/MendelianDisease.md deleted file mode 100644 index 37cc914f5..000000000 --- a/projects/mendelian_disease/docs/MendelianDisease.md +++ /dev/null @@ -1,61 +0,0 @@ - -# Class: MendelianDisease - - - - -URI: [mendelian_disease:MendelianDisease](http://w3id.org/ontogpt/mendelian_disease/MendelianDisease) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Symptom],[Publication],[Onset],[NamedEntity],[Publication]<publications%200..*-++[MendelianDisease|name:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string;label(i):string%20%3F],[Onset]<disease_onsets%200..*-%20[MendelianDisease],[Gene]<genes%200..*-%20[MendelianDisease],[Inheritance]<inheritance%200..1-%20[MendelianDisease],[Symptom]<symptoms%200..*-%20[MendelianDisease],[DiseaseCategory]<subclass_of%200..*-%20[MendelianDisease],[NamedEntity]^-[MendelianDisease],[Inheritance],[Gene],[DiseaseCategory])](https://yuml.me/diagram/nofunky;dir:TB/class/[Symptom],[Publication],[Onset],[NamedEntity],[Publication]<publications%200..*-++[MendelianDisease|name:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string;label(i):string%20%3F],[Onset]<disease_onsets%200..*-%20[MendelianDisease],[Gene]<genes%200..*-%20[MendelianDisease],[Inheritance]<inheritance%200..1-%20[MendelianDisease],[Symptom]<symptoms%200..*-%20[MendelianDisease],[DiseaseCategory]<subclass_of%200..*-%20[MendelianDisease],[NamedEntity]^-[MendelianDisease],[Inheritance],[Gene],[DiseaseCategory]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Attributes - - -### Own - - * [➞name](mendelianDisease__name.md) <sub>0..1</sub> - * Description: the name of the disease - * Range: [String](types/String.md) - * Example: peroxisome biogenesis disorder None - * [➞description](mendelianDisease__description.md) <sub>0..1</sub> - * Description: a description of the disease - * Range: [String](types/String.md) - * Example: Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS) is a group of autosomal recessive disorders affecting the formation of functional peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal degeneration, multiple organ dysfunction and psychomotor impairment None - * [➞synonyms](mendelianDisease__synonyms.md) <sub>0..\*</sub> - * Range: [String](types/String.md) - * Example: Zellweger syndrome spectrum None - * Example: PBD-ZSS None - * [➞subclass_of](mendelianDisease__subclass_of.md) <sub>0..\*</sub> - * Range: [DiseaseCategory](DiseaseCategory.md) - * Example: lysosomal disease None - * Example: autosomal recessive disorder None - * [➞symptoms](mendelianDisease__symptoms.md) <sub>0..\*</sub> - * Range: [Symptom](Symptom.md) - * Example: sensorineural hearing loss None - * Example: pigmentary retinal degeneration None - * [➞inheritance](mendelianDisease__inheritance.md) <sub>0..1</sub> - * Range: [Inheritance](Inheritance.md) - * Example: autosomal recessive None - * [➞genes](mendelianDisease__genes.md) <sub>0..\*</sub> - * Range: [Gene](Gene.md) - * Example: PEX1 None - * Example: PEX2 None - * Example: PEX3 None - * [➞disease_onsets](mendelianDisease__disease_onsets.md) <sub>0..\*</sub> - * Range: [Onset](Onset.md) - * [➞publications](mendelianDisease__publications.md) <sub>0..\*</sub> - * Range: [Publication](Publication.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/NamedEntity.md b/projects/mendelian_disease/docs/NamedEntity.md deleted file mode 100644 index c9f06fce8..000000000 --- a/projects/mendelian_disease/docs/NamedEntity.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [mendelian_disease:NamedEntity](http://w3id.org/ontogpt/mendelian_disease/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Symptom],[RelationshipType],[Onset],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Symptom],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Onset],[NamedEntity]^-[MendelianDisease],[NamedEntity]^-[Inheritance],[NamedEntity]^-[Gene],[NamedEntity]^-[DiseaseCategory],[Triple],[MendelianDisease],[Inheritance],[Gene],[DiseaseCategory])](https://yuml.me/diagram/nofunky;dir:TB/class/[Symptom],[RelationshipType],[Onset],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Symptom],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Onset],[NamedEntity]^-[MendelianDisease],[NamedEntity]^-[Inheritance],[NamedEntity]^-[Gene],[NamedEntity]^-[DiseaseCategory],[Triple],[MendelianDisease],[Inheritance],[Gene],[DiseaseCategory]) - -## Children - - * [DiseaseCategory](DiseaseCategory.md) - * [Gene](Gene.md) - * [Inheritance](Inheritance.md) - * [MendelianDisease](MendelianDisease.md) - * [Onset](Onset.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/NullDataOptions.md b/projects/mendelian_disease/docs/NullDataOptions.md deleted file mode 100644 index 45d64908d..000000000 --- a/projects/mendelian_disease/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [mendelian_disease:NullDataOptions](http://w3id.org/ontogpt/mendelian_disease/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/mendelian_disease/docs/Onset.md b/projects/mendelian_disease/docs/Onset.md deleted file mode 100644 index 71a6c2a4b..000000000 --- a/projects/mendelian_disease/docs/Onset.md +++ /dev/null @@ -1,44 +0,0 @@ - -# Class: Onset - - - - -URI: [mendelian_disease:Onset](http://w3id.org/ontogpt/mendelian_disease/Onset) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[MendelianDisease]-%20disease_onsets%200..*>[Onset|years_old:string%20%3F;decades:string%20*;juvenile_or_adult:string%20%3F;id(i):string;label(i):string%20%3F],[Symptom]-%20onset_of_symptom%200..1>[Onset],[NamedEntity]^-[Onset],[Symptom],[NamedEntity],[MendelianDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[MendelianDisease]-%20disease_onsets%200..*>[Onset|years_old:string%20%3F;decades:string%20*;juvenile_or_adult:string%20%3F;id(i):string;label(i):string%20%3F],[Symptom]-%20onset_of_symptom%200..1>[Onset],[NamedEntity]^-[Onset],[Symptom],[NamedEntity],[MendelianDisease]) - -## Identifier prefixes - - * HP - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞disease_onsets](mendelianDisease__disease_onsets.md)* <sub>0..\*</sub> **[Onset](Onset.md)** - * **None** *[➞onset_of_symptom](symptom__onset_of_symptom.md)* <sub>0..1</sub> **[Onset](Onset.md)** - -## Attributes - - -### Own - - * [➞years_old](onset__years_old.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞decades](onset__decades.md) <sub>0..\*</sub> - * Range: [String](types/String.md) - * [➞juvenile_or_adult](onset__juvenile_or_adult.md) <sub>0..1</sub> - * Range: [String](types/String.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/Publication.md b/projects/mendelian_disease/docs/Publication.md deleted file mode 100644 index d88dd3c5d..000000000 --- a/projects/mendelian_disease/docs/Publication.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Publication - - - - -URI: [mendelian_disease:Publication](http://w3id.org/ontogpt/mendelian_disease/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[MendelianDisease]++-%20publications%200..*>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]++-%20publication%200..1>[Publication],[TextWithTriples],[MendelianDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[MendelianDisease]++-%20publications%200..*>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]++-%20publication%200..1>[Publication],[TextWithTriples],[MendelianDisease]) - -## Referenced by Class - - * **None** *[➞publications](mendelianDisease__publications.md)* <sub>0..\*</sub> **[Publication](Publication.md)** - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/RelationshipType.md b/projects/mendelian_disease/docs/RelationshipType.md deleted file mode 100644 index 5b5a029d2..000000000 --- a/projects/mendelian_disease/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [mendelian_disease:RelationshipType](http://w3id.org/ontogpt/mendelian_disease/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/Symptom.md b/projects/mendelian_disease/docs/Symptom.md deleted file mode 100644 index 76bc00661..000000000 --- a/projects/mendelian_disease/docs/Symptom.md +++ /dev/null @@ -1,45 +0,0 @@ - -# Class: Symptom - - - - -URI: [mendelian_disease:Symptom](http://w3id.org/ontogpt/mendelian_disease/Symptom) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Onset]<onset_of_symptom%200..1-%20[Symptom|characteristic:string%20%3F;affects:string%20%3F;severity:string%20%3F;id(i):string;label(i):string%20%3F],[MendelianDisease]-%20symptoms%200..*>[Symptom],[NamedEntity]^-[Symptom],[Onset],[NamedEntity],[MendelianDisease])](https://yuml.me/diagram/nofunky;dir:TB/class/[Onset]<onset_of_symptom%200..1-%20[Symptom|characteristic:string%20%3F;affects:string%20%3F;severity:string%20%3F;id(i):string;label(i):string%20%3F],[MendelianDisease]-%20symptoms%200..*>[Symptom],[NamedEntity]^-[Symptom],[Onset],[NamedEntity],[MendelianDisease]) - -## Identifier prefixes - - * HP - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞symptoms](mendelianDisease__symptoms.md)* <sub>0..\*</sub> **[Symptom](Symptom.md)** - -## Attributes - - -### Own - - * [➞characteristic](symptom__characteristic.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞affects](symptom__affects.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞severity](symptom__severity.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞onset_of_symptom](symptom__onset_of_symptom.md) <sub>0..1</sub> - * Range: [Onset](Onset.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/mendelian_disease/docs/TextWithTriples.md b/projects/mendelian_disease/docs/TextWithTriples.md deleted file mode 100644 index a6ad6b5eb..000000000 --- a/projects/mendelian_disease/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [mendelian_disease:TextWithTriples](http://w3id.org/ontogpt/mendelian_disease/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/mendelian_disease/docs/Triple.md b/projects/mendelian_disease/docs/Triple.md deleted file mode 100644 index 777bd9538..000000000 --- a/projects/mendelian_disease/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [mendelian_disease:Triple](http://w3id.org/ontogpt/mendelian_disease/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/mendelian_disease/docs/annotatorResult__object_id.md b/projects/mendelian_disease/docs/annotatorResult__object_id.md deleted file mode 100644 index fa20bb770..000000000 --- a/projects/mendelian_disease/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [mendelian_disease:annotatorResult__object_id](http://w3id.org/ontogpt/mendelian_disease/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/mendelian_disease/docs/annotatorResult__object_text.md b/projects/mendelian_disease/docs/annotatorResult__object_text.md deleted file mode 100644 index 49f40997d..000000000 --- a/projects/mendelian_disease/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [mendelian_disease:annotatorResult__object_text](http://w3id.org/ontogpt/mendelian_disease/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/mendelian_disease/docs/annotatorResult__subject_text.md b/projects/mendelian_disease/docs/annotatorResult__subject_text.md deleted file mode 100644 index 4ee88b4ce..000000000 --- a/projects/mendelian_disease/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [mendelian_disease:annotatorResult__subject_text](http://w3id.org/ontogpt/mendelian_disease/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/mendelian_disease/docs/extractionResult__extracted_object.md b/projects/mendelian_disease/docs/extractionResult__extracted_object.md deleted file mode 100644 index 62a9b3631..000000000 --- a/projects/mendelian_disease/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [mendelian_disease:extractionResult__extracted_object](http://w3id.org/ontogpt/mendelian_disease/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/mendelian_disease/docs/extractionResult__input_id.md b/projects/mendelian_disease/docs/extractionResult__input_id.md deleted file mode 100644 index 953c258c2..000000000 --- a/projects/mendelian_disease/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [mendelian_disease:extractionResult__input_id](http://w3id.org/ontogpt/mendelian_disease/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/mendelian_disease/docs/extractionResult__input_text.md b/projects/mendelian_disease/docs/extractionResult__input_text.md deleted file mode 100644 index fb3e5306e..000000000 --- a/projects/mendelian_disease/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [mendelian_disease:extractionResult__input_text](http://w3id.org/ontogpt/mendelian_disease/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/mendelian_disease/docs/extractionResult__input_title.md b/projects/mendelian_disease/docs/extractionResult__input_title.md deleted file mode 100644 index a87e4958f..000000000 --- a/projects/mendelian_disease/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [mendelian_disease:extractionResult__input_title](http://w3id.org/ontogpt/mendelian_disease/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/mendelian_disease/docs/extractionResult__named_entities.md b/projects/mendelian_disease/docs/extractionResult__named_entities.md deleted file mode 100644 index 471ab53d5..000000000 --- a/projects/mendelian_disease/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [mendelian_disease:extractionResult__named_entities](http://w3id.org/ontogpt/mendelian_disease/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/mendelian_disease/docs/extractionResult__prompt.md b/projects/mendelian_disease/docs/extractionResult__prompt.md deleted file mode 100644 index ef8d93525..000000000 --- a/projects/mendelian_disease/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [mendelian_disease:extractionResult__prompt](http://w3id.org/ontogpt/mendelian_disease/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/mendelian_disease/docs/extractionResult__raw_completion_output.md b/projects/mendelian_disease/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index ea64ea51b..000000000 --- a/projects/mendelian_disease/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [mendelian_disease:extractionResult__raw_completion_output](http://w3id.org/ontogpt/mendelian_disease/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/mendelian_disease/docs/mendelianDisease__description.md b/projects/mendelian_disease/docs/mendelianDisease__description.md deleted file mode 100644 index ac56dd5e3..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__description.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: description - - -a description of the disease - -URI: [mendelian_disease:mendelianDisease__description](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__description) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Examples:** | | Example(value='Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS) is a group of autosomal recessive disorders affecting the formation of functional peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal degeneration, multiple organ dysfunction and psychomotor impairment', description=None, object=None) | - diff --git a/projects/mendelian_disease/docs/mendelianDisease__disease_onsets.md b/projects/mendelian_disease/docs/mendelianDisease__disease_onsets.md deleted file mode 100644 index d756e8639..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__disease_onsets.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: disease_onsets - - - - -URI: [mendelian_disease:mendelianDisease__disease_onsets](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__disease_onsets) - - -## Domain and Range - -None → <sub>0..\*</sub> [Onset](Onset.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) diff --git a/projects/mendelian_disease/docs/mendelianDisease__genes.md b/projects/mendelian_disease/docs/mendelianDisease__genes.md deleted file mode 100644 index 5d9a9256b..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__genes.md +++ /dev/null @@ -1,31 +0,0 @@ - -# Slot: genes - - - - -URI: [mendelian_disease:mendelianDisease__genes](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__genes) - - -## Domain and Range - -None → <sub>0..\*</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Examples:** | | Example(value='PEX1', description=None, object=None) | -| | | Example(value='PEX2', description=None, object=None) | -| | | Example(value='PEX3', description=None, object=None) | - diff --git a/projects/mendelian_disease/docs/mendelianDisease__inheritance.md b/projects/mendelian_disease/docs/mendelianDisease__inheritance.md deleted file mode 100644 index c27806f64..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__inheritance.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: inheritance - - - - -URI: [mendelian_disease:mendelianDisease__inheritance](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__inheritance) - - -## Domain and Range - -None → <sub>0..1</sub> [Inheritance](Inheritance.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Examples:** | | Example(value='autosomal recessive', description=None, object=None) | - diff --git a/projects/mendelian_disease/docs/mendelianDisease__name.md b/projects/mendelian_disease/docs/mendelianDisease__name.md deleted file mode 100644 index 817f2b785..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__name.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: name - - -the name of the disease - -URI: [mendelian_disease:mendelianDisease__name](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__name) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Examples:** | | Example(value='peroxisome biogenesis disorder', description=None, object=None) | - diff --git a/projects/mendelian_disease/docs/mendelianDisease__publications.md b/projects/mendelian_disease/docs/mendelianDisease__publications.md deleted file mode 100644 index 5904270c5..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__publications.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publications - - - - -URI: [mendelian_disease:mendelianDisease__publications](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__publications) - - -## Domain and Range - -None → <sub>0..\*</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) diff --git a/projects/mendelian_disease/docs/mendelianDisease__subclass_of.md b/projects/mendelian_disease/docs/mendelianDisease__subclass_of.md deleted file mode 100644 index 7e0188197..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__subclass_of.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: subclass_of - - - - -URI: [mendelian_disease:mendelianDisease__subclass_of](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__subclass_of) - - -## Domain and Range - -None → <sub>0..\*</sub> [DiseaseCategory](DiseaseCategory.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Examples:** | | Example(value='lysosomal disease', description=None, object=None) | -| | | Example(value='autosomal recessive disorder', description=None, object=None) | - diff --git a/projects/mendelian_disease/docs/mendelianDisease__symptoms.md b/projects/mendelian_disease/docs/mendelianDisease__symptoms.md deleted file mode 100644 index 5cab05997..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__symptoms.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: symptoms - - - - -URI: [mendelian_disease:mendelianDisease__symptoms](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__symptoms) - - -## Domain and Range - -None → <sub>0..\*</sub> [Symptom](Symptom.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Examples:** | | Example(value='sensorineural hearing loss', description=None, object=None) | -| | | Example(value='pigmentary retinal degeneration', description=None, object=None) | - diff --git a/projects/mendelian_disease/docs/mendelianDisease__synonyms.md b/projects/mendelian_disease/docs/mendelianDisease__synonyms.md deleted file mode 100644 index 56e200782..000000000 --- a/projects/mendelian_disease/docs/mendelianDisease__synonyms.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Slot: synonyms - - - - -URI: [mendelian_disease:mendelianDisease__synonyms](http://w3id.org/ontogpt/mendelian_disease/mendelianDisease__synonyms) - - -## Domain and Range - -None → <sub>0..\*</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [MendelianDisease](MendelianDisease.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Examples:** | | Example(value='Zellweger syndrome spectrum', description=None, object=None) | -| | | Example(value='PBD-ZSS', description=None, object=None) | - diff --git a/projects/mendelian_disease/docs/mendelian_disease.md b/projects/mendelian_disease/docs/mendelian_disease.md deleted file mode 100644 index 3cd230682..000000000 --- a/projects/mendelian_disease/docs/mendelian_disease.md +++ /dev/null @@ -1,125 +0,0 @@ - -# mendelian_disease-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for GO-CAMs - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [DiseaseCategory](DiseaseCategory.md) - * [Gene](Gene.md) - * [Inheritance](Inheritance.md) - * [MendelianDisease](MendelianDisease.md) - * [Onset](Onset.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞description](mendelianDisease__description.md) - a description of the disease - * [➞disease_onsets](mendelianDisease__disease_onsets.md) - * [➞genes](mendelianDisease__genes.md) - * [➞inheritance](mendelianDisease__inheritance.md) - * [➞name](mendelianDisease__name.md) - the name of the disease - * [➞publications](mendelianDisease__publications.md) - * [➞subclass_of](mendelianDisease__subclass_of.md) - * [➞symptoms](mendelianDisease__symptoms.md) - * [➞synonyms](mendelianDisease__synonyms.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞decades](onset__decades.md) - * [➞juvenile_or_adult](onset__juvenile_or_adult.md) - * [➞years_old](onset__years_old.md) - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞affects](symptom__affects.md) - * [➞characteristic](symptom__characteristic.md) - * [➞onset_of_symptom](symptom__onset_of_symptom.md) - * [➞severity](symptom__severity.md) - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/mendelian_disease/docs/namedEntity__id.md b/projects/mendelian_disease/docs/namedEntity__id.md deleted file mode 100644 index 3c8c9e09c..000000000 --- a/projects/mendelian_disease/docs/namedEntity__id.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [mendelian_disease:namedEntity__id](http://w3id.org/ontogpt/mendelian_disease/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseCategory](DiseaseCategory.md) - * [Gene](Gene.md) - * [Inheritance](Inheritance.md) - * [MendelianDisease](MendelianDisease.md) - * [NamedEntity](NamedEntity.md) - * [Onset](Onset.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/mendelian_disease/docs/namedEntity__label.md b/projects/mendelian_disease/docs/namedEntity__label.md deleted file mode 100644 index 1a0187c2e..000000000 --- a/projects/mendelian_disease/docs/namedEntity__label.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [mendelian_disease:namedEntity__label](http://w3id.org/ontogpt/mendelian_disease/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseCategory](DiseaseCategory.md) - * [Gene](Gene.md) - * [Inheritance](Inheritance.md) - * [MendelianDisease](MendelianDisease.md) - * [NamedEntity](NamedEntity.md) - * [Onset](Onset.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/mendelian_disease/docs/onset__decades.md b/projects/mendelian_disease/docs/onset__decades.md deleted file mode 100644 index 248672244..000000000 --- a/projects/mendelian_disease/docs/onset__decades.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: decades - - - - -URI: [mendelian_disease:onset__decades](http://w3id.org/ontogpt/mendelian_disease/onset__decades) - - -## Domain and Range - -None → <sub>0..\*</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Onset](Onset.md) diff --git a/projects/mendelian_disease/docs/onset__juvenile_or_adult.md b/projects/mendelian_disease/docs/onset__juvenile_or_adult.md deleted file mode 100644 index fed7fbd8d..000000000 --- a/projects/mendelian_disease/docs/onset__juvenile_or_adult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: juvenile_or_adult - - - - -URI: [mendelian_disease:onset__juvenile_or_adult](http://w3id.org/ontogpt/mendelian_disease/onset__juvenile_or_adult) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Onset](Onset.md) diff --git a/projects/mendelian_disease/docs/onset__years_old.md b/projects/mendelian_disease/docs/onset__years_old.md deleted file mode 100644 index 535fb9ae2..000000000 --- a/projects/mendelian_disease/docs/onset__years_old.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: years_old - - - - -URI: [mendelian_disease:onset__years_old](http://w3id.org/ontogpt/mendelian_disease/onset__years_old) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Onset](Onset.md) diff --git a/projects/mendelian_disease/docs/publication__abstract.md b/projects/mendelian_disease/docs/publication__abstract.md deleted file mode 100644 index e3fbd0afc..000000000 --- a/projects/mendelian_disease/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [mendelian_disease:publication__abstract](http://w3id.org/ontogpt/mendelian_disease/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/mendelian_disease/docs/publication__combined_text.md b/projects/mendelian_disease/docs/publication__combined_text.md deleted file mode 100644 index 81ebab273..000000000 --- a/projects/mendelian_disease/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [mendelian_disease:publication__combined_text](http://w3id.org/ontogpt/mendelian_disease/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/mendelian_disease/docs/publication__full_text.md b/projects/mendelian_disease/docs/publication__full_text.md deleted file mode 100644 index c7afbf3e3..000000000 --- a/projects/mendelian_disease/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [mendelian_disease:publication__full_text](http://w3id.org/ontogpt/mendelian_disease/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/mendelian_disease/docs/publication__id.md b/projects/mendelian_disease/docs/publication__id.md deleted file mode 100644 index 3d49da17b..000000000 --- a/projects/mendelian_disease/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [mendelian_disease:publication__id](http://w3id.org/ontogpt/mendelian_disease/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/mendelian_disease/docs/publication__title.md b/projects/mendelian_disease/docs/publication__title.md deleted file mode 100644 index 6fe7c20e6..000000000 --- a/projects/mendelian_disease/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [mendelian_disease:publication__title](http://w3id.org/ontogpt/mendelian_disease/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/mendelian_disease/docs/symptom__affects.md b/projects/mendelian_disease/docs/symptom__affects.md deleted file mode 100644 index 8fc9d6785..000000000 --- a/projects/mendelian_disease/docs/symptom__affects.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: affects - - - - -URI: [mendelian_disease:symptom__affects](http://w3id.org/ontogpt/mendelian_disease/symptom__affects) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Symptom](Symptom.md) diff --git a/projects/mendelian_disease/docs/symptom__characteristic.md b/projects/mendelian_disease/docs/symptom__characteristic.md deleted file mode 100644 index cc13b16bb..000000000 --- a/projects/mendelian_disease/docs/symptom__characteristic.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: characteristic - - - - -URI: [mendelian_disease:symptom__characteristic](http://w3id.org/ontogpt/mendelian_disease/symptom__characteristic) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Symptom](Symptom.md) diff --git a/projects/mendelian_disease/docs/symptom__onset_of_symptom.md b/projects/mendelian_disease/docs/symptom__onset_of_symptom.md deleted file mode 100644 index 4eaa246e0..000000000 --- a/projects/mendelian_disease/docs/symptom__onset_of_symptom.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: onset_of_symptom - - - - -URI: [mendelian_disease:symptom__onset_of_symptom](http://w3id.org/ontogpt/mendelian_disease/symptom__onset_of_symptom) - - -## Domain and Range - -None → <sub>0..1</sub> [Onset](Onset.md) - -## Parents - - -## Children - - -## Used by - - * [Symptom](Symptom.md) diff --git a/projects/mendelian_disease/docs/symptom__severity.md b/projects/mendelian_disease/docs/symptom__severity.md deleted file mode 100644 index 662a68cc5..000000000 --- a/projects/mendelian_disease/docs/symptom__severity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: severity - - - - -URI: [mendelian_disease:symptom__severity](http://w3id.org/ontogpt/mendelian_disease/symptom__severity) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Symptom](Symptom.md) diff --git a/projects/mendelian_disease/docs/textWithTriples__publication.md b/projects/mendelian_disease/docs/textWithTriples__publication.md deleted file mode 100644 index 1a85fb332..000000000 --- a/projects/mendelian_disease/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [mendelian_disease:textWithTriples__publication](http://w3id.org/ontogpt/mendelian_disease/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/mendelian_disease/docs/textWithTriples__triples.md b/projects/mendelian_disease/docs/textWithTriples__triples.md deleted file mode 100644 index 46f8fbe3b..000000000 --- a/projects/mendelian_disease/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [mendelian_disease:textWithTriples__triples](http://w3id.org/ontogpt/mendelian_disease/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/mendelian_disease/docs/triple__object.md b/projects/mendelian_disease/docs/triple__object.md deleted file mode 100644 index 5c3842d75..000000000 --- a/projects/mendelian_disease/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [mendelian_disease:triple__object](http://w3id.org/ontogpt/mendelian_disease/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/mendelian_disease/docs/triple__object_qualifier.md b/projects/mendelian_disease/docs/triple__object_qualifier.md deleted file mode 100644 index f7592b8d8..000000000 --- a/projects/mendelian_disease/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [mendelian_disease:triple__object_qualifier](http://w3id.org/ontogpt/mendelian_disease/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/mendelian_disease/docs/triple__predicate.md b/projects/mendelian_disease/docs/triple__predicate.md deleted file mode 100644 index 9816518d1..000000000 --- a/projects/mendelian_disease/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [mendelian_disease:triple__predicate](http://w3id.org/ontogpt/mendelian_disease/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/mendelian_disease/docs/triple__qualifier.md b/projects/mendelian_disease/docs/triple__qualifier.md deleted file mode 100644 index cbe90e2a1..000000000 --- a/projects/mendelian_disease/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [mendelian_disease:triple__qualifier](http://w3id.org/ontogpt/mendelian_disease/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/mendelian_disease/docs/triple__subject.md b/projects/mendelian_disease/docs/triple__subject.md deleted file mode 100644 index 2843678c0..000000000 --- a/projects/mendelian_disease/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [mendelian_disease:triple__subject](http://w3id.org/ontogpt/mendelian_disease/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/mendelian_disease/docs/triple__subject_qualifier.md b/projects/mendelian_disease/docs/triple__subject_qualifier.md deleted file mode 100644 index c0a7f56a3..000000000 --- a/projects/mendelian_disease/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [mendelian_disease:triple__subject_qualifier](http://w3id.org/ontogpt/mendelian_disease/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/mendelian_disease/docs/types/Boolean.md b/projects/mendelian_disease/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/mendelian_disease/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/mendelian_disease/docs/types/Curie.md b/projects/mendelian_disease/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/mendelian_disease/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/mendelian_disease/docs/types/Date.md b/projects/mendelian_disease/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/mendelian_disease/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/mendelian_disease/docs/types/DateOrDatetime.md b/projects/mendelian_disease/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/mendelian_disease/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/mendelian_disease/docs/types/Datetime.md b/projects/mendelian_disease/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/mendelian_disease/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/mendelian_disease/docs/types/Decimal.md b/projects/mendelian_disease/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/mendelian_disease/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/mendelian_disease/docs/types/Double.md b/projects/mendelian_disease/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/mendelian_disease/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/mendelian_disease/docs/types/Float.md b/projects/mendelian_disease/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/mendelian_disease/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/mendelian_disease/docs/types/Integer.md b/projects/mendelian_disease/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/mendelian_disease/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/mendelian_disease/docs/types/Jsonpath.md b/projects/mendelian_disease/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/mendelian_disease/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/mendelian_disease/docs/types/Jsonpointer.md b/projects/mendelian_disease/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/mendelian_disease/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/mendelian_disease/docs/types/Ncname.md b/projects/mendelian_disease/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/mendelian_disease/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/mendelian_disease/docs/types/Nodeidentifier.md b/projects/mendelian_disease/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/mendelian_disease/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/mendelian_disease/docs/types/Objectidentifier.md b/projects/mendelian_disease/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/mendelian_disease/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/mendelian_disease/docs/types/Sparqlpath.md b/projects/mendelian_disease/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/mendelian_disease/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/mendelian_disease/docs/types/String.md b/projects/mendelian_disease/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/mendelian_disease/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/mendelian_disease/docs/types/Time.md b/projects/mendelian_disease/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/mendelian_disease/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/mendelian_disease/docs/types/Uri.md b/projects/mendelian_disease/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/mendelian_disease/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/mendelian_disease/docs/types/Uriorcurie.md b/projects/mendelian_disease/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/mendelian_disease/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/mendelian_disease/excel/mendelian_disease.xlsx b/projects/mendelian_disease/excel/mendelian_disease.xlsx deleted file mode 100644 index ced006d5b2a2e796475963c351f25374c1bbbf2b..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 10310 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objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type DiseaseCategory - { - id: String! - label: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Gene - { - id: String! - label: String - } - -type Inheritance - { - id: String! - label: String - } - -type MendelianDisease - { - id: String! - label: String - name: String - description: String - synonyms: [String] - subclassOf: [DiseaseCategory] - symptoms: [Symptom] - inheritance: Inheritance - genes: [Gene] - diseaseOnsets: [Onset] - publications: [Publication] - } - -interface NamedEntity - { - id: String! - label: String - } - -type Onset - { - id: String! - label: String - yearsOld: String - decades: [String] - juvenileOrAdult: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type Symptom - { - id: String! - label: String - characteristic: String - affects: String - severity: String - onsetOfSymptom: Onset - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/mendelian_disease/jsonld/mendelian_disease.context.jsonld b/projects/mendelian_disease/jsonld/mendelian_disease.context.jsonld deleted file mode 100644 index 27f1ab073..000000000 --- a/projects/mendelian_disease/jsonld/mendelian_disease.context.jsonld +++ /dev/null @@ -1,151 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:54:35", - "source": "mendelian_disease.yaml" - }, - "@context": { - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "HP": "http://example.org/UNKNOWN/HP/", - "MONDO": "http://example.org/UNKNOWN/MONDO/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "mendelian_disease": "http://w3id.org/ontogpt/mendelian_disease/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/mendelian_disease/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "disease_onsets": { - "@type": "@id" - }, - "genes": { - "@type": "@id" - }, - "inheritance": { - "@type": "@id" - }, - "publications": { - "@type": "@id" - }, - "subclass_of": { - "@type": "@id" - }, - "symptoms": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "onset_of_symptom": { - "@type": "@id" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/mendelian_disease/jsonld/mendelian_disease.jsonld b/projects/mendelian_disease/jsonld/mendelian_disease.jsonld deleted file mode 100644 index 1b839aac1..000000000 --- a/projects/mendelian_disease/jsonld/mendelian_disease.jsonld +++ /dev/null @@ -1,1566 +0,0 @@ -{ - "name": "mendelian_disease-template", - "description": "A template for GO-CAMs", - "title": "GO-CAM Template", - "id": "http://w3id.org/ontogpt/mendelian_disease", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "mendelian_disease", - "prefix_reference": "http://w3id.org/ontogpt/mendelian_disease/" - } - ], - "default_prefix": "mendelian_disease", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "mendelianDisease__name", - "description": "the name of the disease", - "examples": [ - { - "value": "peroxisome biogenesis disorder", - "@type": "Example" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/name", - "alias": "name", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "mendelianDisease__description", - "description": "a description of the disease", - "examples": [ - { - "value": "Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS) is a group of autosomal recessive disorders affecting the formation of functional peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal degeneration, multiple organ dysfunction and psychomotor impairment", - "@type": "Example" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/description", - "alias": "description", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "mendelianDisease__synonyms", - "examples": [ - { - "value": "Zellweger syndrome spectrum", - "@type": "Example" - }, - { - "value": "PBD-ZSS", - "@type": "Example" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/synonyms", - "multivalued": true, - "alias": "synonyms", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "mendelianDisease__subclass_of", - "examples": [ - { - "value": "lysosomal disease", - "@type": "Example" - }, - { - "value": "autosomal recessive disorder", - "@type": "Example" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/subclass_of", - "multivalued": true, - "alias": "subclass_of", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "DiseaseCategory", - "@type": "SlotDefinition" - }, - { - "name": "mendelianDisease__symptoms", - "examples": [ - { - "value": "sensorineural hearing loss", - "@type": "Example" - }, - { - "value": "pigmentary retinal degeneration", - "@type": "Example" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/symptoms", - "multivalued": true, - "alias": "symptoms", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "Symptom", - "@type": "SlotDefinition" - }, - { - "name": "mendelianDisease__inheritance", - "examples": [ - { - "value": "autosomal recessive", - "@type": "Example" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/inheritance", - "alias": "inheritance", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "Inheritance", - "@type": "SlotDefinition" - }, - { - "name": "mendelianDisease__genes", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon separated list of gene symbols; for example: PEX1; PEX2; PEX3", - "@type": "Annotation" - } - ], - "examples": [ - { - "value": "PEX1", - "@type": "Example" - }, - { - "value": "PEX2", - "@type": "Example" - }, - { - "value": "PEX3", - "@type": "Example" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/genes", - "multivalued": true, - "alias": "genes", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "mendelianDisease__disease_onsets", - "annotations": [ - { - "tag": "prompt", - "value": "semi-colon separated list of onsets at which the disease occurs, for example: adult; juvenile; first decade", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/disease_onsets", - "multivalued": true, - "alias": "disease_onsets", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "Onset", - "@type": "SlotDefinition" - }, - { - "name": "mendelianDisease__publications", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/publications", - "multivalued": true, - "alias": "publications", - "owner": "MendelianDisease", - "domain_of": [ - "MendelianDisease" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "symptom__characteristic", - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/characteristic", - "alias": "characteristic", - "owner": "Symptom", - "domain_of": [ - "Symptom" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "symptom__affects", - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/affects", - "alias": "affects", - "owner": "Symptom", - "domain_of": [ - "Symptom" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "symptom__severity", - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/severity", - "alias": "severity", - "owner": "Symptom", - "domain_of": [ - "Symptom" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "symptom__onset_of_symptom", - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/onset_of_symptom", - "alias": "onset_of_symptom", - "owner": "Symptom", - "domain_of": [ - "Symptom" - ], - "range": "Onset", - "@type": "SlotDefinition" - }, - { - "name": "onset__years_old", - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/years_old", - "alias": "years_old", - "owner": "Onset", - "domain_of": [ - "Onset" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "onset__decades", - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/decades", - "multivalued": true, - "alias": "decades", - "owner": "Onset", - "domain_of": [ - "Onset" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "onset__juvenile_or_adult", - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "slot_uri": "http://w3id.org/ontogpt/mendelian_disease/juvenile_or_adult", - "alias": "juvenile_or_adult", - "owner": "Onset", - "domain_of": [ - "Onset" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "MendelianDisease", - "definition_uri": "http://w3id.org/ontogpt/mendelian_disease/MendelianDisease", - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label", - "mendelianDisease__name", - "mendelianDisease__description", - "mendelianDisease__synonyms", - "mendelianDisease__subclass_of", - "mendelianDisease__symptoms", - "mendelianDisease__inheritance", - "mendelianDisease__genes", - "mendelianDisease__disease_onsets", - "mendelianDisease__publications" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "name", - "description": "the name of the disease", - "examples": [ - { - "value": "peroxisome biogenesis disorder", - "@type": "Example" - } - ], - "@type": "SlotDefinition" - }, - { - "name": "description", - "description": "a description of the disease", - "examples": [ - { - "value": "Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS) is a group of autosomal recessive disorders affecting the formation of functional peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal degeneration, multiple organ dysfunction and psychomotor impairment", - "@type": "Example" - } - ], - "@type": "SlotDefinition" - }, - { - "name": "synonyms", - "examples": [ - { - "value": "Zellweger syndrome spectrum", - "@type": "Example" - }, - { - "value": "PBD-ZSS", - "@type": "Example" - } - ], - "multivalued": true, - "@type": "SlotDefinition" - }, - { - "name": "subclass_of", - "examples": [ - { - "value": "lysosomal disease", - "@type": "Example" - }, - { - "value": "autosomal recessive disorder", - "@type": "Example" - } - ], - "multivalued": true, - "range": "DiseaseCategory", - "@type": "SlotDefinition" - }, - { - "name": "symptoms", - "examples": [ - { - "value": "sensorineural hearing loss", - "@type": "Example" - }, - { - "value": "pigmentary retinal degeneration", - "@type": "Example" - } - ], - "multivalued": true, - "range": "Symptom", - "@type": "SlotDefinition" - }, - { - "name": "inheritance", - "examples": [ - { - "value": "autosomal recessive", - "@type": "Example" - } - ], - "range": "Inheritance", - "@type": "SlotDefinition" - }, - { - "name": "genes", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon separated list of gene symbols; for example: PEX1; PEX2; PEX3", - "@type": "Annotation" - } - ], - "examples": [ - { - "value": "PEX1", - "@type": "Example" - }, - { - "value": "PEX2", - "@type": "Example" - }, - { - "value": "PEX3", - "@type": "Example" - } - ], - "multivalued": true, - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "disease_onsets", - "annotations": [ - { - "tag": "prompt", - "value": "semi-colon separated list of onsets at which the disease occurs, for example: adult; juvenile; first decade", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "Onset", - "@type": "SlotDefinition" - }, - { - "name": "publications", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "Publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/mendelian_disease/MendelianDisease", - "@type": "ClassDefinition" - }, - { - "name": "DiseaseCategory", - "id_prefixes": [ - "MONDO" - ], - "definition_uri": "http://w3id.org/ontogpt/mendelian_disease/DiseaseCategory", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:mondo", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/mendelian_disease/DiseaseCategory", - "@type": "ClassDefinition" - }, - { - "name": "Gene", - "id_prefixes": [ - "HGNC" - ], - "definition_uri": "http://w3id.org/ontogpt/mendelian_disease/Gene", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, bioportal:hgnc-nr, sqlite:obo:pr", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/mendelian_disease/Gene", - "@type": "ClassDefinition" - }, - { - "name": "Symptom", - "id_prefixes": [ - "HP" - ], - "definition_uri": "http://w3id.org/ontogpt/mendelian_disease/Symptom", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:hp, sqlite:obo:mondo", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label", - "symptom__characteristic", - "symptom__affects", - "symptom__severity", - "symptom__onset_of_symptom" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "characteristic", - "@type": "SlotDefinition" - }, - { - "name": "affects", - "@type": "SlotDefinition" - }, - { - "name": "severity", - "@type": "SlotDefinition" - }, - { - "name": "onset_of_symptom", - "range": "Onset", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/mendelian_disease/Symptom", - "@type": "ClassDefinition" - }, - { - "name": "Onset", - "id_prefixes": [ - "HP" - ], - "definition_uri": "http://w3id.org/ontogpt/mendelian_disease/Onset", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:hp, sqlite:obo:hsapdv", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label", - "onset__years_old", - "onset__decades", - "onset__juvenile_or_adult" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "years_old", - "@type": "SlotDefinition" - }, - { - "name": "decades", - "multivalued": true, - "@type": "SlotDefinition" - }, - { - "name": "juvenile_or_adult", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/mendelian_disease/Onset", - "@type": "ClassDefinition" - }, - { - "name": "Inheritance", - "definition_uri": "http://w3id.org/ontogpt/mendelian_disease/Inheritance", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:hp, sqlite:obo:geno", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/mendelian_disease", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/mendelian_disease/Inheritance", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "mendelian_disease.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 3130, - "generation_date": "2023-08-07T10:54:36", - "@type": "SchemaDefinition", - "@context": [ - "projects/mendelian_disease/jsonld/mendelian_disease.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/mendelian_disease/" - } - ] -} diff --git a/projects/mendelian_disease/jsonschema/mendelian_disease.schema.json b/projects/mendelian_disease/jsonschema/mendelian_disease.schema.json deleted file mode 100644 index beda78946..000000000 --- a/projects/mendelian_disease/jsonschema/mendelian_disease.schema.json +++ /dev/null @@ -1,326 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "DiseaseCategory": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "DiseaseCategory", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Gene": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Gene", - "type": "object" - }, - "Inheritance": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Inheritance", - "type": "object" - }, - "MendelianDisease": { - "additionalProperties": false, - "description": "", - "properties": { - "description": { - "description": "a description of the disease", - "type": "string" - }, - "disease_onsets": { - "items": { - "type": "string" - }, - "type": "array" - }, - "genes": { - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "inheritance": { - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - }, - "name": { - "description": "the name of the disease", - "type": "string" - }, - "publications": { - "items": { - "$ref": "#/$defs/Publication" - }, - "type": "array" - }, - "subclass_of": { - "items": { - "type": "string" - }, - "type": "array" - }, - "symptoms": { - "items": { - "type": "string" - }, - "type": "array" - }, - "synonyms": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "id" - ], - "title": "MendelianDisease", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Onset": { - "additionalProperties": false, - "description": "", - "properties": { - "decades": { - "items": { - "type": "string" - }, - "type": "array" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "juvenile_or_adult": { - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - }, - "years_old": { - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Onset", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "Symptom": { - "additionalProperties": false, - "description": "", - "properties": { - "affects": { - "type": "string" - }, - "characteristic": { - "type": "string" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - }, - "onset_of_symptom": { - "type": "string" - }, - "severity": { - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Symptom", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/mendelian_disease", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "mendelian_disease-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/mendelian_disease/mendelian_disease.py b/projects/mendelian_disease/mendelian_disease.py deleted file mode 100644 index 277925b8b..000000000 --- a/projects/mendelian_disease/mendelian_disease.py +++ /dev/null @@ -1,628 +0,0 @@ -# Auto generated from mendelian_disease.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:54:43 -# Schema: mendelian_disease-template -# -# id: http://w3id.org/ontogpt/mendelian_disease -# description: A template for GO-CAMs -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -HGNC = CurieNamespace('HGNC', 'http://example.org/UNKNOWN/HGNC/') -HP = CurieNamespace('HP', 'http://example.org/UNKNOWN/HP/') -MONDO = CurieNamespace('MONDO', 'http://example.org/UNKNOWN/MONDO/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -MENDELIAN_DISEASE = CurieNamespace('mendelian_disease', 'http://w3id.org/ontogpt/mendelian_disease/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = MENDELIAN_DISEASE - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class MendelianDiseaseId(NamedEntityId): - pass - - -class DiseaseCategoryId(NamedEntityId): - pass - - -class GeneId(NamedEntityId): - pass - - -class SymptomId(NamedEntityId): - pass - - -class OnsetId(NamedEntityId): - pass - - -class InheritanceId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class MendelianDisease(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.MendelianDisease - class_class_curie: ClassVar[str] = "mendelian_disease:MendelianDisease" - class_name: ClassVar[str] = "MendelianDisease" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.MendelianDisease - - id: Union[str, MendelianDiseaseId] = None - name: Optional[str] = None - description: Optional[str] = None - synonyms: Optional[Union[str, List[str]]] = empty_list() - subclass_of: Optional[Union[Union[str, DiseaseCategoryId], List[Union[str, DiseaseCategoryId]]]] = empty_list() - symptoms: Optional[Union[Union[str, SymptomId], List[Union[str, SymptomId]]]] = empty_list() - inheritance: Optional[Union[str, InheritanceId]] = None - genes: Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]] = empty_list() - disease_onsets: Optional[Union[Union[str, OnsetId], List[Union[str, OnsetId]]]] = empty_list() - publications: Optional[Union[Union[dict, "Publication"], List[Union[dict, "Publication"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MendelianDiseaseId): - self.id = MendelianDiseaseId(self.id) - - if self.name is not None and not isinstance(self.name, str): - self.name = str(self.name) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.synonyms, list): - self.synonyms = [self.synonyms] if self.synonyms is not None else [] - self.synonyms = [v if isinstance(v, str) else str(v) for v in self.synonyms] - - if not isinstance(self.subclass_of, list): - self.subclass_of = [self.subclass_of] if self.subclass_of is not None else [] - self.subclass_of = [v if isinstance(v, DiseaseCategoryId) else DiseaseCategoryId(v) for v in self.subclass_of] - - if not isinstance(self.symptoms, list): - self.symptoms = [self.symptoms] if self.symptoms is not None else [] - self.symptoms = [v if isinstance(v, SymptomId) else SymptomId(v) for v in self.symptoms] - - if self.inheritance is not None and not isinstance(self.inheritance, InheritanceId): - self.inheritance = InheritanceId(self.inheritance) - - if not isinstance(self.genes, list): - self.genes = [self.genes] if self.genes is not None else [] - self.genes = [v if isinstance(v, GeneId) else GeneId(v) for v in self.genes] - - if not isinstance(self.disease_onsets, list): - self.disease_onsets = [self.disease_onsets] if self.disease_onsets is not None else [] - self.disease_onsets = [v if isinstance(v, OnsetId) else OnsetId(v) for v in self.disease_onsets] - - if not isinstance(self.publications, list): - self.publications = [self.publications] if self.publications is not None else [] - self.publications = [v if isinstance(v, Publication) else Publication(**as_dict(v)) for v in self.publications] - - super().__post_init__(**kwargs) - - -@dataclass -class DiseaseCategory(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.DiseaseCategory - class_class_curie: ClassVar[str] = "mendelian_disease:DiseaseCategory" - class_name: ClassVar[str] = "DiseaseCategory" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.DiseaseCategory - - id: Union[str, DiseaseCategoryId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiseaseCategoryId): - self.id = DiseaseCategoryId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Gene - class_class_curie: ClassVar[str] = "mendelian_disease:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Symptom(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Symptom - class_class_curie: ClassVar[str] = "mendelian_disease:Symptom" - class_name: ClassVar[str] = "Symptom" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Symptom - - id: Union[str, SymptomId] = None - characteristic: Optional[str] = None - affects: Optional[str] = None - severity: Optional[str] = None - onset_of_symptom: Optional[Union[str, OnsetId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, SymptomId): - self.id = SymptomId(self.id) - - if self.characteristic is not None and not isinstance(self.characteristic, str): - self.characteristic = str(self.characteristic) - - if self.affects is not None and not isinstance(self.affects, str): - self.affects = str(self.affects) - - if self.severity is not None and not isinstance(self.severity, str): - self.severity = str(self.severity) - - if self.onset_of_symptom is not None and not isinstance(self.onset_of_symptom, OnsetId): - self.onset_of_symptom = OnsetId(self.onset_of_symptom) - - super().__post_init__(**kwargs) - - -@dataclass -class Onset(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Onset - class_class_curie: ClassVar[str] = "mendelian_disease:Onset" - class_name: ClassVar[str] = "Onset" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Onset - - id: Union[str, OnsetId] = None - years_old: Optional[str] = None - decades: Optional[Union[str, List[str]]] = empty_list() - juvenile_or_adult: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OnsetId): - self.id = OnsetId(self.id) - - if self.years_old is not None and not isinstance(self.years_old, str): - self.years_old = str(self.years_old) - - if not isinstance(self.decades, list): - self.decades = [self.decades] if self.decades is not None else [] - self.decades = [v if isinstance(v, str) else str(v) for v in self.decades] - - if self.juvenile_or_adult is not None and not isinstance(self.juvenile_or_adult, str): - self.juvenile_or_adult = str(self.juvenile_or_adult) - - super().__post_init__(**kwargs) - - -@dataclass -class Inheritance(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Inheritance - class_class_curie: ClassVar[str] = "mendelian_disease:Inheritance" - class_name: ClassVar[str] = "Inheritance" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Inheritance - - id: Union[str, InheritanceId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, InheritanceId): - self.id = InheritanceId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = MENDELIAN_DISEASE.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.mendelianDisease__name = Slot(uri=MENDELIAN_DISEASE.name, name="mendelianDisease__name", curie=MENDELIAN_DISEASE.curie('name'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__name, domain=None, range=Optional[str]) - -slots.mendelianDisease__description = Slot(uri=MENDELIAN_DISEASE.description, name="mendelianDisease__description", curie=MENDELIAN_DISEASE.curie('description'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__description, domain=None, range=Optional[str]) - -slots.mendelianDisease__synonyms = Slot(uri=MENDELIAN_DISEASE.synonyms, name="mendelianDisease__synonyms", curie=MENDELIAN_DISEASE.curie('synonyms'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__synonyms, domain=None, range=Optional[Union[str, List[str]]]) - -slots.mendelianDisease__subclass_of = Slot(uri=MENDELIAN_DISEASE.subclass_of, name="mendelianDisease__subclass_of", curie=MENDELIAN_DISEASE.curie('subclass_of'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__subclass_of, domain=None, range=Optional[Union[Union[str, DiseaseCategoryId], List[Union[str, DiseaseCategoryId]]]]) - -slots.mendelianDisease__symptoms = Slot(uri=MENDELIAN_DISEASE.symptoms, name="mendelianDisease__symptoms", curie=MENDELIAN_DISEASE.curie('symptoms'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__symptoms, domain=None, range=Optional[Union[Union[str, SymptomId], List[Union[str, SymptomId]]]]) - -slots.mendelianDisease__inheritance = Slot(uri=MENDELIAN_DISEASE.inheritance, name="mendelianDisease__inheritance", curie=MENDELIAN_DISEASE.curie('inheritance'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__inheritance, domain=None, range=Optional[Union[str, InheritanceId]]) - -slots.mendelianDisease__genes = Slot(uri=MENDELIAN_DISEASE.genes, name="mendelianDisease__genes", curie=MENDELIAN_DISEASE.curie('genes'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__genes, domain=None, range=Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]]) - -slots.mendelianDisease__disease_onsets = Slot(uri=MENDELIAN_DISEASE.disease_onsets, name="mendelianDisease__disease_onsets", curie=MENDELIAN_DISEASE.curie('disease_onsets'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__disease_onsets, domain=None, range=Optional[Union[Union[str, OnsetId], List[Union[str, OnsetId]]]]) - -slots.mendelianDisease__publications = Slot(uri=MENDELIAN_DISEASE.publications, name="mendelianDisease__publications", curie=MENDELIAN_DISEASE.curie('publications'), - model_uri=MENDELIAN_DISEASE.mendelianDisease__publications, domain=None, range=Optional[Union[Union[dict, Publication], List[Union[dict, Publication]]]]) - -slots.symptom__characteristic = Slot(uri=MENDELIAN_DISEASE.characteristic, name="symptom__characteristic", curie=MENDELIAN_DISEASE.curie('characteristic'), - model_uri=MENDELIAN_DISEASE.symptom__characteristic, domain=None, range=Optional[str]) - -slots.symptom__affects = Slot(uri=MENDELIAN_DISEASE.affects, name="symptom__affects", curie=MENDELIAN_DISEASE.curie('affects'), - model_uri=MENDELIAN_DISEASE.symptom__affects, domain=None, range=Optional[str]) - -slots.symptom__severity = Slot(uri=MENDELIAN_DISEASE.severity, name="symptom__severity", curie=MENDELIAN_DISEASE.curie('severity'), - model_uri=MENDELIAN_DISEASE.symptom__severity, domain=None, range=Optional[str]) - -slots.symptom__onset_of_symptom = Slot(uri=MENDELIAN_DISEASE.onset_of_symptom, name="symptom__onset_of_symptom", curie=MENDELIAN_DISEASE.curie('onset_of_symptom'), - model_uri=MENDELIAN_DISEASE.symptom__onset_of_symptom, domain=None, range=Optional[Union[str, OnsetId]]) - -slots.onset__years_old = Slot(uri=MENDELIAN_DISEASE.years_old, name="onset__years_old", curie=MENDELIAN_DISEASE.curie('years_old'), - model_uri=MENDELIAN_DISEASE.onset__years_old, domain=None, range=Optional[str]) - -slots.onset__decades = Slot(uri=MENDELIAN_DISEASE.decades, name="onset__decades", curie=MENDELIAN_DISEASE.curie('decades'), - model_uri=MENDELIAN_DISEASE.onset__decades, domain=None, range=Optional[Union[str, List[str]]]) - -slots.onset__juvenile_or_adult = Slot(uri=MENDELIAN_DISEASE.juvenile_or_adult, name="onset__juvenile_or_adult", curie=MENDELIAN_DISEASE.curie('juvenile_or_adult'), - model_uri=MENDELIAN_DISEASE.onset__juvenile_or_adult, domain=None, range=Optional[str]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=MENDELIAN_DISEASE.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=MENDELIAN_DISEASE.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=MENDELIAN_DISEASE.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=MENDELIAN_DISEASE.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=MENDELIAN_DISEASE.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=MENDELIAN_DISEASE.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=MENDELIAN_DISEASE.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=MENDELIAN_DISEASE.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=MENDELIAN_DISEASE.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=MENDELIAN_DISEASE.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=MENDELIAN_DISEASE.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=MENDELIAN_DISEASE.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=MENDELIAN_DISEASE.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=MENDELIAN_DISEASE.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=MENDELIAN_DISEASE.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=MENDELIAN_DISEASE.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=MENDELIAN_DISEASE.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=MENDELIAN_DISEASE.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=MENDELIAN_DISEASE.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=MENDELIAN_DISEASE.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=MENDELIAN_DISEASE.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=MENDELIAN_DISEASE.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=MENDELIAN_DISEASE.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=MENDELIAN_DISEASE.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=MENDELIAN_DISEASE.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/mendelian_disease/owl/mendelian_disease.owl.ttl b/projects/mendelian_disease/owl/mendelian_disease.owl.ttl deleted file mode 100644 index 48a74b2a0..000000000 --- a/projects/mendelian_disease/owl/mendelian_disease.owl.ttl +++ /dev/null @@ -1,542 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix mendelian_disease: <http://w3id.org/ontogpt/mendelian_disease/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/mendelian_disease> a owl:Ontology ; - rdfs:label "mendelian_disease-template" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples> ; - linkml:classes "{'MendelianDisease': ClassDefinition(name='MendelianDisease', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/mendelian_disease/MendelianDisease', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/mendelian_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label', 'mendelianDisease__name', 'mendelianDisease__description', 'mendelianDisease__synonyms', 'mendelianDisease__subclass_of', 'mendelianDisease__symptoms', 'mendelianDisease__inheritance', 'mendelianDisease__genes', 'mendelianDisease__disease_onsets', 'mendelianDisease__publications'], slot_usage={}, attributes={'name': SlotDefinition(name='name', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='peroxisome biogenesis disorder', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a description of the disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS) is a group of autosomal recessive disorders affecting the formation of functional peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal degeneration, multiple organ dysfunction and psychomotor impairment', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='Zellweger syndrome spectrum', description=None, object=None), Example(value='PBD-ZSS', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='lysosomal disease', description=None, object=None), Example(value='autosomal recessive disorder', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DiseaseCategory', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'symptoms': SlotDefinition(name='symptoms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='sensorineural hearing loss', description=None, object=None), Example(value='pigmentary retinal degeneration', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Symptom', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'inheritance': SlotDefinition(name='inheritance', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='autosomal recessive', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Inheritance', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon separated list of gene symbols; for example: PEX1; PEX2; PEX3', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='PEX1', description=None, object=None), Example(value='PEX2', description=None, object=None), Example(value='PEX3', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'disease_onsets': SlotDefinition(name='disease_onsets', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semi-colon separated list of onsets at which the disease occurs, for example: adult; juvenile; first decade', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Onset', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'publications': SlotDefinition(name='publications', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='mendelian_disease:MendelianDisease', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'DiseaseCategory': ClassDefinition(name='DiseaseCategory', id_prefixes=['MONDO'], definition_uri='http://w3id.org/ontogpt/mendelian_disease/DiseaseCategory', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:mondo', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/mendelian_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='mendelian_disease:DiseaseCategory', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC'], definition_uri='http://w3id.org/ontogpt/mendelian_disease/Gene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, bioportal:hgnc-nr, sqlite:obo:pr', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/mendelian_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='mendelian_disease:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Symptom': ClassDefinition(name='Symptom', id_prefixes=['HP'], definition_uri='http://w3id.org/ontogpt/mendelian_disease/Symptom', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hp, sqlite:obo:mondo', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/mendelian_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label', 'symptom__characteristic', 'symptom__affects', 'symptom__severity', 'symptom__onset_of_symptom'], slot_usage={}, attributes={'characteristic': SlotDefinition(name='characteristic', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'affects': SlotDefinition(name='affects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'severity': SlotDefinition(name='severity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'onset_of_symptom': SlotDefinition(name='onset_of_symptom', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Onset', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='mendelian_disease:Symptom', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Onset': ClassDefinition(name='Onset', id_prefixes=['HP'], definition_uri='http://w3id.org/ontogpt/mendelian_disease/Onset', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hp, sqlite:obo:hsapdv', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/mendelian_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label', 'onset__years_old', 'onset__decades', 'onset__juvenile_or_adult'], slot_usage={}, attributes={'years_old': SlotDefinition(name='years_old', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decades': SlotDefinition(name='decades', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'juvenile_or_adult': SlotDefinition(name='juvenile_or_adult', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='mendelian_disease:Onset', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Inheritance': ClassDefinition(name='Inheritance', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/mendelian_disease/Inheritance', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hp, sqlite:obo:geno', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/mendelian_disease', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='mendelian_disease:Inheritance', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/mendelian_disease" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -mendelian_disease:MendelianDisease a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MendelianDisease" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom mendelian_disease:DiseaseCategory ; - owl:onProperty mendelian_disease:subclass_of ], - [ a owl:Restriction ; - owl:allValuesFrom mendelian_disease:Gene ; - owl:onProperty mendelian_disease:genes ], - [ a owl:Restriction ; - owl:allValuesFrom mendelian_disease:Onset ; - owl:onProperty mendelian_disease:disease_onsets ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty mendelian_disease:name ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty mendelian_disease:description ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass mendelian_disease:Inheritance ; - owl:onProperty mendelian_disease:inheritance ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty mendelian_disease:publications ], - [ a owl:Restriction ; - owl:allValuesFrom mendelian_disease:Symptom ; - owl:onProperty mendelian_disease:symptoms ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty mendelian_disease:synonyms ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{'name': SlotDefinition(name='name', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='peroxisome biogenesis disorder', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a description of the disease', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='Peroxisome biogenesis disorders, Zellweger syndrome spectrum (PBD-ZSS) is a group of autosomal recessive disorders affecting the formation of functional peroxisomes, characterized by sensorineural hearing loss, pigmentary retinal degeneration, multiple organ dysfunction and psychomotor impairment', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='Zellweger syndrome spectrum', description=None, object=None), Example(value='PBD-ZSS', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='lysosomal disease', description=None, object=None), Example(value='autosomal recessive disorder', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='DiseaseCategory', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'symptoms': SlotDefinition(name='symptoms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='sensorineural hearing loss', description=None, object=None), Example(value='pigmentary retinal degeneration', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Symptom', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'inheritance': SlotDefinition(name='inheritance', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='autosomal recessive', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Inheritance', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon separated list of gene symbols; for example: PEX1; PEX2; PEX3', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[Example(value='PEX1', description=None, object=None), Example(value='PEX2', description=None, object=None), Example(value='PEX3', description=None, object=None)], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'disease_onsets': SlotDefinition(name='disease_onsets', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semi-colon separated list of onsets at which the disease occurs, for example: adult; juvenile; first decade', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Onset', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'publications': SlotDefinition(name='publications', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - mendelian_disease:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -mendelian_disease:affects a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "affects" ; - rdfs:range linkml:String . - -mendelian_disease:characteristic a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "characteristic" ; - rdfs:range linkml:String . - -mendelian_disease:decades a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "decades" ; - rdfs:range linkml:String . - -mendelian_disease:description a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "description" ; - rdfs:range linkml:String ; - skos:definition "a description of the disease" . - -mendelian_disease:disease_onsets a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "disease_onsets" ; - mendelian_disease:prompt "semi-colon separated list of onsets at which the disease occurs, for example: adult; juvenile; first decade" ; - rdfs:range mendelian_disease:Onset . - -mendelian_disease:genes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "genes" ; - mendelian_disease:prompt "semicolon separated list of gene symbols; for example: PEX1; PEX2; PEX3" ; - rdfs:range mendelian_disease:Gene . - -mendelian_disease:inheritance a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "inheritance" ; - rdfs:range mendelian_disease:Inheritance . - -mendelian_disease:juvenile_or_adult a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "juvenile_or_adult" ; - rdfs:range linkml:String . - -mendelian_disease:name a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "name" ; - rdfs:range linkml:String ; - skos:definition "the name of the disease" . - -mendelian_disease:onset_of_symptom a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "onset_of_symptom" ; - rdfs:range mendelian_disease:Onset . - -mendelian_disease:publications a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publications" ; - mendelian_disease:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -mendelian_disease:severity a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "severity" ; - rdfs:range linkml:String . - -mendelian_disease:subclass_of a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subclass_of" ; - rdfs:range mendelian_disease:DiseaseCategory . - -mendelian_disease:symptoms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "symptoms" ; - rdfs:range mendelian_disease:Symptom . - -mendelian_disease:synonyms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "synonyms" ; - rdfs:range linkml:String . - -mendelian_disease:years_old a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "years_old" ; - rdfs:range linkml:String . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - mendelian_disease:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -mendelian_disease:DiseaseCategory a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DiseaseCategory" ; - mendelian_disease:annotators "sqlite:obo:mondo" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -mendelian_disease:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - mendelian_disease:annotators "gilda:, bioportal:hgnc-nr, sqlite:obo:pr" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -mendelian_disease:Inheritance a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Inheritance" ; - mendelian_disease:annotators "sqlite:obo:hp, sqlite:obo:geno" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -mendelian_disease:Symptom a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Symptom" ; - mendelian_disease:annotators "sqlite:obo:hp, sqlite:obo:mondo" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty mendelian_disease:severity ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty mendelian_disease:characteristic ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass mendelian_disease:Onset ; - owl:onProperty mendelian_disease:onset_of_symptom ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty mendelian_disease:affects ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{'characteristic': SlotDefinition(name='characteristic', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'affects': SlotDefinition(name='affects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'severity': SlotDefinition(name='severity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'onset_of_symptom': SlotDefinition(name='onset_of_symptom', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Onset', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -mendelian_disease:Onset a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Onset" ; - mendelian_disease:annotators "sqlite:obo:hp, sqlite:obo:hsapdv" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty mendelian_disease:decades ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty mendelian_disease:years_old ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty mendelian_disease:juvenile_or_adult ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{'years_old': SlotDefinition(name='years_old', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decades': SlotDefinition(name='decades', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'juvenile_or_adult': SlotDefinition(name='juvenile_or_adult', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/mendelian_disease/prefixmap/mendelian_disease.yaml b/projects/mendelian_disease/prefixmap/mendelian_disease.yaml deleted file mode 100644 index 5e93eefe8..000000000 --- a/projects/mendelian_disease/prefixmap/mendelian_disease.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{ - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "HP": "http://example.org/UNKNOWN/HP/", - "MONDO": "http://example.org/UNKNOWN/MONDO/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "mendelian_disease": "http://w3id.org/ontogpt/mendelian_disease/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/mendelian_disease/protobuf/mendelian_disease.proto b/projects/mendelian_disease/protobuf/mendelian_disease.proto deleted file mode 100644 index 8f5aa1ee5..000000000 --- a/projects/mendelian_disease/protobuf/mendelian_disease.proto +++ /dev/null @@ -1,81 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message DiseaseCategory - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -message Inheritance - { - string id = 0 - string label = 0 - } -message MendelianDisease - { - string id = 0 - string label = 0 - string name = 0 - string description = 0 - repeated string synonyms = 0 - repeated diseaseCategory subclassOf = 0 - repeated symptom symptoms = 0 - inheritance inheritance = 0 - repeated gene genes = 0 - repeated onset diseaseOnsets = 0 - repeated publication publications = 0 - } -message Onset - { - string id = 0 - string label = 0 - string yearsOld = 0 - repeated string decades = 0 - string juvenileOrAdult = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message Symptom - { - string id = 0 - string label = 0 - string characteristic = 0 - string affects = 0 - string severity = 0 - onset onsetOfSymptom = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/mendelian_disease/shacl/mendelian_disease.shacl.ttl b/projects/mendelian_disease/shacl/mendelian_disease.shacl.ttl deleted file mode 100644 index 2768d35bc..000000000 --- a/projects/mendelian_disease/shacl/mendelian_disease.shacl.ttl +++ /dev/null @@ -1,305 +0,0 @@ -@prefix linkml: <https://w3id.org/linkml/> . -@prefix mendelian_disease: <http://w3id.org/ontogpt/mendelian_disease/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ], - [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -mendelian_disease:MendelianDisease a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:nodeKind sh:BlankNode ; - sh:order 8 ; - sh:path mendelian_disease:publications ], - [ sh:class mendelian_disease:Gene ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path mendelian_disease:genes ], - [ sh:class mendelian_disease:Inheritance ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path mendelian_disease:inheritance ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 10 ; - sh:path <rdfs:label> ], - [ sh:description "a description of the disease" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path mendelian_disease:description ], - [ sh:class mendelian_disease:Onset ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path mendelian_disease:disease_onsets ], - [ sh:class mendelian_disease:Symptom ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path mendelian_disease:symptoms ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:order 2 ; - sh:path mendelian_disease:synonyms ], - [ sh:class mendelian_disease:DiseaseCategory ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path mendelian_disease:subclass_of ], - [ sh:description "the name of the disease" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path mendelian_disease:name ] ; - sh:targetClass mendelian_disease:MendelianDisease . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -mendelian_disease:DiseaseCategory a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass mendelian_disease:DiseaseCategory . - -mendelian_disease:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass mendelian_disease:Gene . - -mendelian_disease:Inheritance a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass mendelian_disease:Inheritance . - -mendelian_disease:Symptom a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path <rdfs:label> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path mendelian_disease:affects ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path mendelian_disease:characteristic ], - [ sh:class mendelian_disease:Onset ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path mendelian_disease:onset_of_symptom ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path mendelian_disease:severity ] ; - sh:targetClass mendelian_disease:Symptom . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -mendelian_disease:Onset a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:order 1 ; - sh:path mendelian_disease:decades ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <rdfs:label> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path mendelian_disease:years_old ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path mendelian_disease:juvenile_or_adult ] ; - sh:targetClass mendelian_disease:Onset . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/mendelian_disease/shex/mendelian_disease.shex b/projects/mendelian_disease/shex/mendelian_disease.shex deleted file mode 100644 index 6fe919d0a..000000000 --- a/projects/mendelian_disease/shex/mendelian_disease.shex +++ /dev/null @@ -1,198 +0,0 @@ -BASE <http://w3id.org/ontogpt/mendelian_disease/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -<DiseaseCategory> CLOSED { - ( $<DiseaseCategory_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <DiseaseCategory> ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<Gene> CLOSED { - ( $<Gene_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Gene> ] - ) -} - -<Inheritance> CLOSED { - ( $<Inheritance_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Inheritance> ] - ) -} - -<MendelianDisease> CLOSED { - ( $<MendelianDisease_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - <name> @linkml:String ? ; - <description> @linkml:String ? ; - <synonyms> @linkml:String * ; - <subclass_of> @<DiseaseCategory> * ; - <symptoms> @<Symptom> * ; - <inheritance> @<Inheritance> ? ; - <genes> @<Gene> * ; - <disease_onsets> @<Onset> * ; - <publications> @core:Publication * - ) ; - rdf:type [ <MendelianDisease> ] - ) -} - -core:NamedEntity ( - @<DiseaseCategory> OR @<Gene> OR @<Inheritance> OR @<MendelianDisease> OR @<Onset> OR @core:RelationshipType OR @<Symptom> -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<Onset> CLOSED { - ( $<Onset_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - <years_old> @linkml:String ? ; - <decades> @linkml:String * ; - <juvenile_or_adult> @linkml:String ? - ) ; - rdf:type [ <Onset> ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -<Symptom> CLOSED { - ( $<Symptom_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - <characteristic> @linkml:String ? ; - <affects> @linkml:String ? ; - <severity> @linkml:String ? ; - <onset_of_symptom> @<Onset> ? - ) ; - rdf:type [ <Symptom> ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/mendelian_disease/sqlschema/mendelian_disease.sql b/projects/mendelian_disease/sqlschema/mendelian_disease.sql deleted file mode 100644 index 260e51602..000000000 --- a/projects/mendelian_disease/sqlschema/mendelian_disease.sql +++ /dev/null @@ -1,109 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Inheritance" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Onset" ( - id TEXT NOT NULL, - label TEXT, - years_old TEXT, - juvenile_or_adult TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "MendelianDisease" ( - id TEXT NOT NULL, - label TEXT, - name TEXT, - description TEXT, - inheritance TEXT, - disease_onsets TEXT, - publications TEXT, - PRIMARY KEY (id), - FOREIGN KEY(inheritance) REFERENCES "Inheritance" (id) -); - -CREATE TABLE "Onset_decades" ( - backref_id TEXT, - decades TEXT, - PRIMARY KEY (backref_id, decades), - FOREIGN KEY(backref_id) REFERENCES "Onset" (id) -); - -CREATE TABLE "DiseaseCategory" ( - id TEXT NOT NULL, - label TEXT, - "MendelianDisease_id" TEXT, - PRIMARY KEY (id), - FOREIGN KEY("MendelianDisease_id") REFERENCES "MendelianDisease" (id) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - "MendelianDisease_id" TEXT, - PRIMARY KEY (id), - FOREIGN KEY("MendelianDisease_id") REFERENCES "MendelianDisease" (id) -); - -CREATE TABLE "Symptom" ( - id TEXT NOT NULL, - label TEXT, - characteristic TEXT, - affects TEXT, - severity TEXT, - onset_of_symptom TEXT, - "MendelianDisease_id" TEXT, - PRIMARY KEY (id), - FOREIGN KEY(onset_of_symptom) REFERENCES "Onset" (id), - FOREIGN KEY("MendelianDisease_id") REFERENCES "MendelianDisease" (id) -); - -CREATE TABLE "MendelianDisease_synonyms" ( - backref_id TEXT, - synonyms TEXT, - PRIMARY KEY (backref_id, synonyms), - FOREIGN KEY(backref_id) REFERENCES "MendelianDisease" (id) -); diff --git a/projects/metabolic_process/docs/AnnotatorResult.md b/projects/metabolic_process/docs/AnnotatorResult.md deleted file mode 100644 index 8d5a8c586..000000000 --- a/projects/metabolic_process/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [bp:AnnotatorResult](http://w3id.org/ontogpt/metabolic-process-templateAnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/metabolic_process/docs/Any.md b/projects/metabolic_process/docs/Any.md deleted file mode 100644 index e5c3dde82..000000000 --- a/projects/metabolic_process/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [bp:Any](http://w3id.org/ontogpt/metabolic-process-templateAny) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/metabolic_process/docs/ChemicalEntity.md b/projects/metabolic_process/docs/ChemicalEntity.md deleted file mode 100644 index a8f5e0622..000000000 --- a/projects/metabolic_process/docs/ChemicalEntity.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: ChemicalEntity - - - - -URI: [bp:ChemicalEntity](http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MetabolicProcess]-%20inputs%200..*>[ChemicalEntity|id(i):string;label(i):string%20%3F],[MetabolicProcess]-%20outputs%200..*>[ChemicalEntity],[NamedEntity]^-[ChemicalEntity],[MetabolicProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MetabolicProcess]-%20inputs%200..*>[ChemicalEntity|id(i):string;label(i):string%20%3F],[MetabolicProcess]-%20outputs%200..*>[ChemicalEntity],[NamedEntity]^-[ChemicalEntity],[MetabolicProcess]) - -## Identifier prefixes - - * CHEBI - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞inputs](metabolicProcess__inputs.md)* <sub>0..\*</sub> **[ChemicalEntity](ChemicalEntity.md)** - * **None** *[➞outputs](metabolicProcess__outputs.md)* <sub>0..\*</sub> **[ChemicalEntity](ChemicalEntity.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metabolic_process/docs/CompoundExpression.md b/projects/metabolic_process/docs/CompoundExpression.md deleted file mode 100644 index b0af5e420..000000000 --- a/projects/metabolic_process/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [bp:CompoundExpression](http://w3id.org/ontogpt/metabolic-process-templateCompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/metabolic_process/docs/ExtractionResult.md b/projects/metabolic_process/docs/ExtractionResult.md deleted file mode 100644 index 71ffeafef..000000000 --- a/projects/metabolic_process/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [bp:ExtractionResult](http://w3id.org/ontogpt/metabolic-process-templateExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/metabolic_process/docs/MetabolicProcess.md b/projects/metabolic_process/docs/MetabolicProcess.md deleted file mode 100644 index abcdacc70..000000000 --- a/projects/metabolic_process/docs/MetabolicProcess.md +++ /dev/null @@ -1,47 +0,0 @@ - -# Class: MetabolicProcess - - - - -URI: [bp:MetabolicProcess](http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcess) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MetabolicProcessCategory],[ChemicalEntity]<outputs%200..*-%20[MetabolicProcess|label:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string],[ChemicalEntity]<inputs%200..*-%20[MetabolicProcess],[MetabolicProcessCategory]<category%200..1-%20[MetabolicProcess],[MetabolicProcessCategory]<subclass_of%200..*-%20[MetabolicProcess],[NamedEntity]^-[MetabolicProcess],[ChemicalEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MetabolicProcessCategory],[ChemicalEntity]<outputs%200..*-%20[MetabolicProcess|label:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string],[ChemicalEntity]<inputs%200..*-%20[MetabolicProcess],[MetabolicProcessCategory]<category%200..1-%20[MetabolicProcess],[MetabolicProcessCategory]<subclass_of%200..*-%20[MetabolicProcess],[NamedEntity]^-[MetabolicProcess],[ChemicalEntity]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Attributes - - -### Own - - * [➞label](metabolicProcess__label.md) <sub>0..1</sub> - * Description: the name of the metabolic process - * Range: [String](types/String.md) - * [➞description](metabolicProcess__description.md) <sub>0..1</sub> - * Description: a textual description of the metabolic process - * Range: [String](types/String.md) - * [➞synonyms](metabolicProcess__synonyms.md) <sub>0..\*</sub> - * Description: alternative names of the metabolic process - * Range: [String](types/String.md) - * [➞subclass_of](metabolicProcess__subclass_of.md) <sub>0..\*</sub> - * Description: a semicolon separated list of broader metabolic processes which this is a subclass of - * Range: [MetabolicProcessCategory](MetabolicProcessCategory.md) - * [➞category](metabolicProcess__category.md) <sub>0..1</sub> - * Description: the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity - * Range: [MetabolicProcessCategory](MetabolicProcessCategory.md) - * [➞inputs](metabolicProcess__inputs.md) <sub>0..\*</sub> - * Description: the inputs of the metabolic process - * Range: [ChemicalEntity](ChemicalEntity.md) - * [➞outputs](metabolicProcess__outputs.md) <sub>0..\*</sub> - * Description: the outputs of the metabolic process - * Range: [ChemicalEntity](ChemicalEntity.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) diff --git a/projects/metabolic_process/docs/MetabolicProcessCategory.md b/projects/metabolic_process/docs/MetabolicProcessCategory.md deleted file mode 100644 index 12c2b0a05..000000000 --- a/projects/metabolic_process/docs/MetabolicProcessCategory.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: MetabolicProcessCategory - - - - -URI: [bp:MetabolicProcessCategory](http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MetabolicProcess]-%20category%200..1>[MetabolicProcessCategory|id(i):string;label(i):string%20%3F],[MetabolicProcess]-%20subclass_of%200..*>[MetabolicProcessCategory],[NamedEntity]^-[MetabolicProcessCategory],[MetabolicProcess])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[MetabolicProcess]-%20category%200..1>[MetabolicProcessCategory|id(i):string;label(i):string%20%3F],[MetabolicProcess]-%20subclass_of%200..*>[MetabolicProcessCategory],[NamedEntity]^-[MetabolicProcessCategory],[MetabolicProcess]) - -## Identifier prefixes - - * GO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞category](metabolicProcess__category.md)* <sub>0..1</sub> **[MetabolicProcessCategory](MetabolicProcessCategory.md)** - * **None** *[➞subclass_of](metabolicProcess__subclass_of.md)* <sub>0..\*</sub> **[MetabolicProcessCategory](MetabolicProcessCategory.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metabolic_process/docs/NamedEntity.md b/projects/metabolic_process/docs/NamedEntity.md deleted file mode 100644 index 331cb7183..000000000 --- a/projects/metabolic_process/docs/NamedEntity.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [bp:NamedEntity](http://w3id.org/ontogpt/metabolic-process-templateNamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[MetabolicProcessCategory],[NamedEntity]^-[MetabolicProcess],[NamedEntity]^-[ChemicalEntity],[Triple],[MetabolicProcessCategory],[MetabolicProcess],[ChemicalEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[MetabolicProcessCategory],[NamedEntity]^-[MetabolicProcess],[NamedEntity]^-[ChemicalEntity],[Triple],[MetabolicProcessCategory],[MetabolicProcess],[ChemicalEntity]) - -## Children - - * [ChemicalEntity](ChemicalEntity.md) - * [MetabolicProcess](MetabolicProcess.md) - * [MetabolicProcessCategory](MetabolicProcessCategory.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metabolic_process/docs/NullDataOptions.md b/projects/metabolic_process/docs/NullDataOptions.md deleted file mode 100644 index 3edea6d1c..000000000 --- a/projects/metabolic_process/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [bp:NullDataOptions](http://w3id.org/ontogpt/metabolic-process-templateNullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/metabolic_process/docs/Publication.md b/projects/metabolic_process/docs/Publication.md deleted file mode 100644 index 76e1d2fb7..000000000 --- a/projects/metabolic_process/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [bp:Publication](http://w3id.org/ontogpt/metabolic-process-templatePublication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/metabolic_process/docs/RelationshipType.md b/projects/metabolic_process/docs/RelationshipType.md deleted file mode 100644 index 36a6d4172..000000000 --- a/projects/metabolic_process/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [bp:RelationshipType](http://w3id.org/ontogpt/metabolic-process-templateRelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metabolic_process/docs/TextWithTriples.md b/projects/metabolic_process/docs/TextWithTriples.md deleted file mode 100644 index e6131d139..000000000 --- a/projects/metabolic_process/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [bp:TextWithTriples](http://w3id.org/ontogpt/metabolic-process-templateTextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/metabolic_process/docs/Triple.md b/projects/metabolic_process/docs/Triple.md deleted file mode 100644 index 157ba54c5..000000000 --- a/projects/metabolic_process/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [bp:Triple](http://w3id.org/ontogpt/metabolic-process-templateTriple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/metabolic_process/docs/annotatorResult__object_id.md b/projects/metabolic_process/docs/annotatorResult__object_id.md deleted file mode 100644 index 0ed3b4a01..000000000 --- a/projects/metabolic_process/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [bp:annotatorResult__object_id](http://w3id.org/ontogpt/metabolic-process-templateannotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/metabolic_process/docs/annotatorResult__object_text.md b/projects/metabolic_process/docs/annotatorResult__object_text.md deleted file mode 100644 index 077cd93fc..000000000 --- a/projects/metabolic_process/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [bp:annotatorResult__object_text](http://w3id.org/ontogpt/metabolic-process-templateannotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/metabolic_process/docs/annotatorResult__subject_text.md b/projects/metabolic_process/docs/annotatorResult__subject_text.md deleted file mode 100644 index 8f258d90c..000000000 --- a/projects/metabolic_process/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [bp:annotatorResult__subject_text](http://w3id.org/ontogpt/metabolic-process-templateannotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/metabolic_process/docs/extractionResult__extracted_object.md b/projects/metabolic_process/docs/extractionResult__extracted_object.md deleted file mode 100644 index 054936032..000000000 --- a/projects/metabolic_process/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [bp:extractionResult__extracted_object](http://w3id.org/ontogpt/metabolic-process-templateextractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metabolic_process/docs/extractionResult__input_id.md b/projects/metabolic_process/docs/extractionResult__input_id.md deleted file mode 100644 index ed6f1bc59..000000000 --- a/projects/metabolic_process/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [bp:extractionResult__input_id](http://w3id.org/ontogpt/metabolic-process-templateextractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metabolic_process/docs/extractionResult__input_text.md b/projects/metabolic_process/docs/extractionResult__input_text.md deleted file mode 100644 index 8f76b8a42..000000000 --- a/projects/metabolic_process/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [bp:extractionResult__input_text](http://w3id.org/ontogpt/metabolic-process-templateextractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metabolic_process/docs/extractionResult__input_title.md b/projects/metabolic_process/docs/extractionResult__input_title.md deleted file mode 100644 index bc462f4a2..000000000 --- a/projects/metabolic_process/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [bp:extractionResult__input_title](http://w3id.org/ontogpt/metabolic-process-templateextractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metabolic_process/docs/extractionResult__named_entities.md b/projects/metabolic_process/docs/extractionResult__named_entities.md deleted file mode 100644 index 2af9f84a2..000000000 --- a/projects/metabolic_process/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [bp:extractionResult__named_entities](http://w3id.org/ontogpt/metabolic-process-templateextractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metabolic_process/docs/extractionResult__prompt.md b/projects/metabolic_process/docs/extractionResult__prompt.md deleted file mode 100644 index 815243606..000000000 --- a/projects/metabolic_process/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [bp:extractionResult__prompt](http://w3id.org/ontogpt/metabolic-process-templateextractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metabolic_process/docs/extractionResult__raw_completion_output.md b/projects/metabolic_process/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 31fd1e0d9..000000000 --- a/projects/metabolic_process/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [bp:extractionResult__raw_completion_output](http://w3id.org/ontogpt/metabolic-process-templateextractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metabolic_process/docs/metabolicProcess__category.md b/projects/metabolic_process/docs/metabolicProcess__category.md deleted file mode 100644 index f33c38406..000000000 --- a/projects/metabolic_process/docs/metabolicProcess__category.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: category - - -the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity - -URI: [bp:metabolicProcess__category](http://w3id.org/ontogpt/metabolic-process-templatemetabolicProcess__category) - - -## Domain and Range - -None → <sub>0..1</sub> [MetabolicProcessCategory](MetabolicProcessCategory.md) - -## Parents - - -## Children - - -## Used by - - * [MetabolicProcess](MetabolicProcess.md) diff --git a/projects/metabolic_process/docs/metabolicProcess__description.md b/projects/metabolic_process/docs/metabolicProcess__description.md deleted file mode 100644 index cb5beec0b..000000000 --- a/projects/metabolic_process/docs/metabolicProcess__description.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: description - - -a textual description of the metabolic process - -URI: [bp:metabolicProcess__description](http://w3id.org/ontogpt/metabolic-process-templatemetabolicProcess__description) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [MetabolicProcess](MetabolicProcess.md) diff --git a/projects/metabolic_process/docs/metabolicProcess__inputs.md b/projects/metabolic_process/docs/metabolicProcess__inputs.md deleted file mode 100644 index 83efb9168..000000000 --- a/projects/metabolic_process/docs/metabolicProcess__inputs.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: inputs - - -the inputs of the metabolic process - -URI: [bp:metabolicProcess__inputs](http://w3id.org/ontogpt/metabolic-process-templatemetabolicProcess__inputs) - - -## Domain and Range - -None → <sub>0..\*</sub> [ChemicalEntity](ChemicalEntity.md) - -## Parents - - -## Children - - -## Used by - - * [MetabolicProcess](MetabolicProcess.md) diff --git a/projects/metabolic_process/docs/metabolicProcess__label.md b/projects/metabolic_process/docs/metabolicProcess__label.md deleted file mode 100644 index 69ec93d09..000000000 --- a/projects/metabolic_process/docs/metabolicProcess__label.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: label - - -the name of the metabolic process - -URI: [bp:metabolicProcess__label](http://w3id.org/ontogpt/metabolic-process-templatemetabolicProcess__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [MetabolicProcess](MetabolicProcess.md) diff --git a/projects/metabolic_process/docs/metabolicProcess__outputs.md b/projects/metabolic_process/docs/metabolicProcess__outputs.md deleted file mode 100644 index 8fd1808fe..000000000 --- a/projects/metabolic_process/docs/metabolicProcess__outputs.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: outputs - - -the outputs of the metabolic process - -URI: [bp:metabolicProcess__outputs](http://w3id.org/ontogpt/metabolic-process-templatemetabolicProcess__outputs) - - -## Domain and Range - -None → <sub>0..\*</sub> [ChemicalEntity](ChemicalEntity.md) - -## Parents - - -## Children - - -## Used by - - * [MetabolicProcess](MetabolicProcess.md) diff --git a/projects/metabolic_process/docs/metabolicProcess__subclass_of.md b/projects/metabolic_process/docs/metabolicProcess__subclass_of.md deleted file mode 100644 index 3995a93e5..000000000 --- a/projects/metabolic_process/docs/metabolicProcess__subclass_of.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subclass_of - - -a semicolon separated list of broader metabolic processes which this is a subclass of - -URI: [bp:metabolicProcess__subclass_of](http://w3id.org/ontogpt/metabolic-process-templatemetabolicProcess__subclass_of) - - -## Domain and Range - -None → <sub>0..\*</sub> [MetabolicProcessCategory](MetabolicProcessCategory.md) - -## Parents - - -## Children - - -## Used by - - * [MetabolicProcess](MetabolicProcess.md) diff --git a/projects/metabolic_process/docs/metabolicProcess__synonyms.md b/projects/metabolic_process/docs/metabolicProcess__synonyms.md deleted file mode 100644 index bd9819ea2..000000000 --- a/projects/metabolic_process/docs/metabolicProcess__synonyms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: synonyms - - -alternative names of the metabolic process - -URI: [bp:metabolicProcess__synonyms](http://w3id.org/ontogpt/metabolic-process-templatemetabolicProcess__synonyms) - - -## Domain and Range - -None → <sub>0..\*</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [MetabolicProcess](MetabolicProcess.md) diff --git a/projects/metabolic_process/docs/metabolic_process.md b/projects/metabolic_process/docs/metabolic_process.md deleted file mode 100644 index 2244dfb4c..000000000 --- a/projects/metabolic_process/docs/metabolic_process.md +++ /dev/null @@ -1,113 +0,0 @@ - -# metabolic-process-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for GO-CAMs - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [ChemicalEntity](ChemicalEntity.md) - * [MetabolicProcess](MetabolicProcess.md) - * [MetabolicProcessCategory](MetabolicProcessCategory.md) - * [RelationshipType](RelationshipType.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞category](metabolicProcess__category.md) - the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity - * [➞description](metabolicProcess__description.md) - a textual description of the metabolic process - * [➞inputs](metabolicProcess__inputs.md) - the inputs of the metabolic process - * [➞label](metabolicProcess__label.md) - the name of the metabolic process - * [➞outputs](metabolicProcess__outputs.md) - the outputs of the metabolic process - * [➞subclass_of](metabolicProcess__subclass_of.md) - a semicolon separated list of broader metabolic processes which this is a subclass of - * [➞synonyms](metabolicProcess__synonyms.md) - alternative names of the metabolic process - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/metabolic_process/docs/namedEntity__id.md b/projects/metabolic_process/docs/namedEntity__id.md deleted file mode 100644 index 7d07dc170..000000000 --- a/projects/metabolic_process/docs/namedEntity__id.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [bp:namedEntity__id](http://w3id.org/ontogpt/metabolic-process-templatenamedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ChemicalEntity](ChemicalEntity.md) - * [MetabolicProcess](MetabolicProcess.md) - * [MetabolicProcessCategory](MetabolicProcessCategory.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/metabolic_process/docs/namedEntity__label.md b/projects/metabolic_process/docs/namedEntity__label.md deleted file mode 100644 index 3921b7438..000000000 --- a/projects/metabolic_process/docs/namedEntity__label.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [bp:namedEntity__label](http://w3id.org/ontogpt/metabolic-process-templatenamedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ChemicalEntity](ChemicalEntity.md) - * [MetabolicProcessCategory](MetabolicProcessCategory.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/metabolic_process/docs/publication__abstract.md b/projects/metabolic_process/docs/publication__abstract.md deleted file mode 100644 index d95c3bb6e..000000000 --- a/projects/metabolic_process/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [bp:publication__abstract](http://w3id.org/ontogpt/metabolic-process-templatepublication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metabolic_process/docs/publication__combined_text.md b/projects/metabolic_process/docs/publication__combined_text.md deleted file mode 100644 index cea215db8..000000000 --- a/projects/metabolic_process/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [bp:publication__combined_text](http://w3id.org/ontogpt/metabolic-process-templatepublication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metabolic_process/docs/publication__full_text.md b/projects/metabolic_process/docs/publication__full_text.md deleted file mode 100644 index c5baca387..000000000 --- a/projects/metabolic_process/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [bp:publication__full_text](http://w3id.org/ontogpt/metabolic-process-templatepublication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metabolic_process/docs/publication__id.md b/projects/metabolic_process/docs/publication__id.md deleted file mode 100644 index 41e717748..000000000 --- a/projects/metabolic_process/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [bp:publication__id](http://w3id.org/ontogpt/metabolic-process-templatepublication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metabolic_process/docs/publication__title.md b/projects/metabolic_process/docs/publication__title.md deleted file mode 100644 index 3f1cac98a..000000000 --- a/projects/metabolic_process/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [bp:publication__title](http://w3id.org/ontogpt/metabolic-process-templatepublication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metabolic_process/docs/textWithTriples__publication.md b/projects/metabolic_process/docs/textWithTriples__publication.md deleted file mode 100644 index f488281e7..000000000 --- a/projects/metabolic_process/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [bp:textWithTriples__publication](http://w3id.org/ontogpt/metabolic-process-templatetextWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/metabolic_process/docs/textWithTriples__triples.md b/projects/metabolic_process/docs/textWithTriples__triples.md deleted file mode 100644 index 3be3a12b5..000000000 --- a/projects/metabolic_process/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [bp:textWithTriples__triples](http://w3id.org/ontogpt/metabolic-process-templatetextWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/metabolic_process/docs/triple__object.md b/projects/metabolic_process/docs/triple__object.md deleted file mode 100644 index 5cb142a08..000000000 --- a/projects/metabolic_process/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [bp:triple__object](http://w3id.org/ontogpt/metabolic-process-templatetriple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metabolic_process/docs/triple__object_qualifier.md b/projects/metabolic_process/docs/triple__object_qualifier.md deleted file mode 100644 index 17474aa33..000000000 --- a/projects/metabolic_process/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [bp:triple__object_qualifier](http://w3id.org/ontogpt/metabolic-process-templatetriple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metabolic_process/docs/triple__predicate.md b/projects/metabolic_process/docs/triple__predicate.md deleted file mode 100644 index 65d5544da..000000000 --- a/projects/metabolic_process/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [bp:triple__predicate](http://w3id.org/ontogpt/metabolic-process-templatetriple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metabolic_process/docs/triple__qualifier.md b/projects/metabolic_process/docs/triple__qualifier.md deleted file mode 100644 index f1a43c11a..000000000 --- a/projects/metabolic_process/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [bp:triple__qualifier](http://w3id.org/ontogpt/metabolic-process-templatetriple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metabolic_process/docs/triple__subject.md b/projects/metabolic_process/docs/triple__subject.md deleted file mode 100644 index 28e17194c..000000000 --- a/projects/metabolic_process/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [bp:triple__subject](http://w3id.org/ontogpt/metabolic-process-templatetriple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metabolic_process/docs/triple__subject_qualifier.md b/projects/metabolic_process/docs/triple__subject_qualifier.md deleted file mode 100644 index 3880349e6..000000000 --- a/projects/metabolic_process/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [bp:triple__subject_qualifier](http://w3id.org/ontogpt/metabolic-process-templatetriple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metabolic_process/docs/types/Boolean.md b/projects/metabolic_process/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/metabolic_process/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/metabolic_process/docs/types/Curie.md b/projects/metabolic_process/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/metabolic_process/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/metabolic_process/docs/types/Date.md b/projects/metabolic_process/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/metabolic_process/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/metabolic_process/docs/types/DateOrDatetime.md b/projects/metabolic_process/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/metabolic_process/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/metabolic_process/docs/types/Datetime.md b/projects/metabolic_process/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/metabolic_process/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/metabolic_process/docs/types/Decimal.md b/projects/metabolic_process/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/metabolic_process/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/metabolic_process/docs/types/Double.md b/projects/metabolic_process/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/metabolic_process/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/metabolic_process/docs/types/Float.md b/projects/metabolic_process/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/metabolic_process/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/metabolic_process/docs/types/Integer.md b/projects/metabolic_process/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/metabolic_process/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/metabolic_process/docs/types/Jsonpath.md b/projects/metabolic_process/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/metabolic_process/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/metabolic_process/docs/types/Jsonpointer.md b/projects/metabolic_process/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/metabolic_process/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/metabolic_process/docs/types/Ncname.md b/projects/metabolic_process/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/metabolic_process/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/metabolic_process/docs/types/Nodeidentifier.md b/projects/metabolic_process/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/metabolic_process/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/metabolic_process/docs/types/Objectidentifier.md b/projects/metabolic_process/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/metabolic_process/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/metabolic_process/docs/types/Sparqlpath.md b/projects/metabolic_process/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/metabolic_process/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/metabolic_process/docs/types/String.md b/projects/metabolic_process/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/metabolic_process/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/metabolic_process/docs/types/Time.md b/projects/metabolic_process/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/metabolic_process/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/metabolic_process/docs/types/Uri.md b/projects/metabolic_process/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/metabolic_process/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/metabolic_process/docs/types/Uriorcurie.md b/projects/metabolic_process/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/metabolic_process/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/metabolic_process/excel/metabolic_process.xlsx b/projects/metabolic_process/excel/metabolic_process.xlsx deleted file mode 100644 index 3e2f8fd73f47a0649309c437b26d8c08f8f9e483..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 8761 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extractedObject: Any - namedEntities: [Any] - } - -type MetabolicProcess - { - id: String! - label: String - description: String - synonyms: [String] - subclassOf: [MetabolicProcessCategory] - category: MetabolicProcessCategory - inputs: [ChemicalEntity] - outputs: [ChemicalEntity] - } - -type MetabolicProcessCategory - { - id: String! - label: String - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/metabolic_process/jsonld/metabolic_process.context.jsonld b/projects/metabolic_process/jsonld/metabolic_process.context.jsonld deleted file mode 100644 index 6f0736682..000000000 --- a/projects/metabolic_process/jsonld/metabolic_process.context.jsonld +++ /dev/null @@ -1,144 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:54:48", - "source": "metabolic_process.yaml" - }, - "@context": { - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "GO": "http://example.org/UNKNOWN/GO/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "bp": { - "@id": "http://w3id.org/ontogpt/metabolic-process-template", - "@prefix": true - }, - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/metabolic-process-template", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "category": { - "@type": "@id" - }, - "inputs": { - "@type": "@id" - }, - "outputs": { - "@type": "@id" - }, - "subclass_of": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/metabolic_process/jsonld/metabolic_process.jsonld b/projects/metabolic_process/jsonld/metabolic_process.jsonld deleted file mode 100644 index 4612d8f3c..000000000 --- a/projects/metabolic_process/jsonld/metabolic_process.jsonld +++ /dev/null @@ -1,1176 +0,0 @@ -{ - "name": "metabolic-process-template", - "description": "A template for GO-CAMs", - "title": "metabolic Process Template", - "id": "https://w3id.org/ontogpt/metabolic_process", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "bp", - "prefix_reference": "http://w3id.org/ontogpt/metabolic-process-template" - } - ], - "default_prefix": "bp", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "metabolicProcess__label", - "description": "the name of the metabolic process", - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "slot_uri": "http://w3id.org/ontogpt/metabolic-process-templatelabel", - "alias": "label", - "owner": "MetabolicProcess", - "domain_of": [ - "MetabolicProcess" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "metabolicProcess__description", - "description": "a textual description of the metabolic process", - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "slot_uri": "http://w3id.org/ontogpt/metabolic-process-templatedescription", - "alias": "description", - "owner": "MetabolicProcess", - "domain_of": [ - "MetabolicProcess" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "metabolicProcess__synonyms", - "description": "alternative names of the metabolic process", - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "slot_uri": "http://w3id.org/ontogpt/metabolic-process-templatesynonyms", - "multivalued": true, - "alias": "synonyms", - "owner": "MetabolicProcess", - "domain_of": [ - "MetabolicProcess" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "metabolicProcess__subclass_of", - "description": "a semicolon separated list of broader metabolic processes which this is a subclass of", - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "slot_uri": "http://w3id.org/ontogpt/metabolic-process-templatesubclass_of", - "multivalued": true, - "alias": "subclass_of", - "owner": "MetabolicProcess", - "domain_of": [ - "MetabolicProcess" - ], - "range": "MetabolicProcessCategory", - "@type": "SlotDefinition" - }, - { - "name": "metabolicProcess__category", - "description": "the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity", - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "slot_uri": "http://w3id.org/ontogpt/metabolic-process-templatecategory", - "alias": "category", - "owner": "MetabolicProcess", - "domain_of": [ - "MetabolicProcess" - ], - "range": "MetabolicProcessCategory", - "@type": "SlotDefinition" - }, - { - "name": "metabolicProcess__inputs", - "description": "the inputs of the metabolic process", - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "slot_uri": "http://w3id.org/ontogpt/metabolic-process-templateinputs", - "multivalued": true, - "alias": "inputs", - "owner": "MetabolicProcess", - "domain_of": [ - "MetabolicProcess" - ], - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "metabolicProcess__outputs", - "description": "the outputs of the metabolic process", - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "slot_uri": "http://w3id.org/ontogpt/metabolic-process-templateoutputs", - "multivalued": true, - "alias": "outputs", - "owner": "MetabolicProcess", - "domain_of": [ - "MetabolicProcess" - ], - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "MetabolicProcess", - "definition_uri": "http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcess", - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "metabolicProcess__label", - "metabolicProcess__description", - "metabolicProcess__synonyms", - "metabolicProcess__subclass_of", - "metabolicProcess__category", - "metabolicProcess__inputs", - "metabolicProcess__outputs" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "label", - "description": "the name of the metabolic process", - "@type": "SlotDefinition" - }, - { - "name": "description", - "description": "a textual description of the metabolic process", - "@type": "SlotDefinition" - }, - { - "name": "synonyms", - "description": "alternative names of the metabolic process", - "multivalued": true, - "@type": "SlotDefinition" - }, - { - "name": "subclass_of", - "description": "a semicolon separated list of broader metabolic processes which this is a subclass of", - "multivalued": true, - "range": "MetabolicProcessCategory", - "@type": "SlotDefinition" - }, - { - "name": "category", - "description": "the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity", - "range": "MetabolicProcessCategory", - "@type": "SlotDefinition" - }, - { - "name": "inputs", - "description": "the inputs of the metabolic process", - "multivalued": true, - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "outputs", - "description": "the outputs of the metabolic process", - "multivalued": true, - "range": "ChemicalEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcess", - "@type": "ClassDefinition" - }, - { - "name": "MetabolicProcessCategory", - "id_prefixes": [ - "GO" - ], - "definition_uri": "http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory", - "@type": "ClassDefinition" - }, - { - "name": "ChemicalEntity", - "id_prefixes": [ - "CHEBI" - ], - "definition_uri": "http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:chebi", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/metabolic_process", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "metabolic_process.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 1633, - "generation_date": "2023-08-07T10:54:49", - "@type": "SchemaDefinition", - "@context": [ - "projects/metabolic_process/jsonld/metabolic_process.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/metabolic-process-template" - } - ] -} diff --git a/projects/metabolic_process/jsonschema/metabolic_process.schema.json b/projects/metabolic_process/jsonschema/metabolic_process.schema.json deleted file mode 100644 index f29a0837e..000000000 --- a/projects/metabolic_process/jsonschema/metabolic_process.schema.json +++ /dev/null @@ -1,234 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ChemicalEntity": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ChemicalEntity", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "MetabolicProcess": { - "additionalProperties": false, - "description": "", - "properties": { - "category": { - "description": "the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity", - "type": "string" - }, - "description": { - "description": "a textual description of the metabolic process", - "type": "string" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "inputs": { - "description": "the inputs of the metabolic process", - "items": { - "type": "string" - }, - "type": "array" - }, - "label": { - "description": "the name of the metabolic process", - "type": "string" - }, - "outputs": { - "description": "the outputs of the metabolic process", - "items": { - "type": "string" - }, - "type": "array" - }, - "subclass_of": { - "description": "a semicolon separated list of broader metabolic processes which this is a subclass of", - "items": { - "type": "string" - }, - "type": "array" - }, - "synonyms": { - "description": "alternative names of the metabolic process", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "id" - ], - "title": "MetabolicProcess", - "type": "object" - }, - "MetabolicProcessCategory": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "MetabolicProcessCategory", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "https://w3id.org/ontogpt/metabolic_process", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "metabolic-process-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/metabolic_process/metabolic_process.py b/projects/metabolic_process/metabolic_process.py deleted file mode 100644 index fbbb06585..000000000 --- a/projects/metabolic_process/metabolic_process.py +++ /dev/null @@ -1,489 +0,0 @@ -# Auto generated from metabolic_process.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:54:56 -# Schema: metabolic-process-template -# -# id: https://w3id.org/ontogpt/metabolic_process -# description: A template for GO-CAMs -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CHEBI = CurieNamespace('CHEBI', 'http://example.org/UNKNOWN/CHEBI/') -GO = CurieNamespace('GO', 'http://example.org/UNKNOWN/GO/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -BP = CurieNamespace('bp', 'http://w3id.org/ontogpt/metabolic-process-template') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = BP - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class MetabolicProcessId(NamedEntityId): - pass - - -class MetabolicProcessCategoryId(NamedEntityId): - pass - - -class ChemicalEntityId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = BP.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = BP.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class MetabolicProcess(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.MetabolicProcess - class_class_curie: ClassVar[str] = "bp:MetabolicProcess" - class_name: ClassVar[str] = "MetabolicProcess" - class_model_uri: ClassVar[URIRef] = BP.MetabolicProcess - - id: Union[str, MetabolicProcessId] = None - label: Optional[str] = None - description: Optional[str] = None - synonyms: Optional[Union[str, List[str]]] = empty_list() - subclass_of: Optional[Union[Union[str, MetabolicProcessCategoryId], List[Union[str, MetabolicProcessCategoryId]]]] = empty_list() - category: Optional[Union[str, MetabolicProcessCategoryId]] = None - inputs: Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]] = empty_list() - outputs: Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MetabolicProcessId): - self.id = MetabolicProcessId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.synonyms, list): - self.synonyms = [self.synonyms] if self.synonyms is not None else [] - self.synonyms = [v if isinstance(v, str) else str(v) for v in self.synonyms] - - if not isinstance(self.subclass_of, list): - self.subclass_of = [self.subclass_of] if self.subclass_of is not None else [] - self.subclass_of = [v if isinstance(v, MetabolicProcessCategoryId) else MetabolicProcessCategoryId(v) for v in self.subclass_of] - - if self.category is not None and not isinstance(self.category, MetabolicProcessCategoryId): - self.category = MetabolicProcessCategoryId(self.category) - - if not isinstance(self.inputs, list): - self.inputs = [self.inputs] if self.inputs is not None else [] - self.inputs = [v if isinstance(v, ChemicalEntityId) else ChemicalEntityId(v) for v in self.inputs] - - if not isinstance(self.outputs, list): - self.outputs = [self.outputs] if self.outputs is not None else [] - self.outputs = [v if isinstance(v, ChemicalEntityId) else ChemicalEntityId(v) for v in self.outputs] - - super().__post_init__(**kwargs) - - -@dataclass -class MetabolicProcessCategory(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.MetabolicProcessCategory - class_class_curie: ClassVar[str] = "bp:MetabolicProcessCategory" - class_name: ClassVar[str] = "MetabolicProcessCategory" - class_model_uri: ClassVar[URIRef] = BP.MetabolicProcessCategory - - id: Union[str, MetabolicProcessCategoryId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MetabolicProcessCategoryId): - self.id = MetabolicProcessCategoryId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalEntity(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = BP.ChemicalEntity - class_class_curie: ClassVar[str] = "bp:ChemicalEntity" - class_name: ClassVar[str] = "ChemicalEntity" - class_model_uri: ClassVar[URIRef] = BP.ChemicalEntity - - id: Union[str, ChemicalEntityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalEntityId): - self.id = ChemicalEntityId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = BP.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = BP.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = BP.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = BP.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = BP.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = BP.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.metabolicProcess__label = Slot(uri=BP.label, name="metabolicProcess__label", curie=BP.curie('label'), - model_uri=BP.metabolicProcess__label, domain=None, range=Optional[str]) - -slots.metabolicProcess__description = Slot(uri=BP.description, name="metabolicProcess__description", curie=BP.curie('description'), - model_uri=BP.metabolicProcess__description, domain=None, range=Optional[str]) - -slots.metabolicProcess__synonyms = Slot(uri=BP.synonyms, name="metabolicProcess__synonyms", curie=BP.curie('synonyms'), - model_uri=BP.metabolicProcess__synonyms, domain=None, range=Optional[Union[str, List[str]]]) - -slots.metabolicProcess__subclass_of = Slot(uri=BP.subclass_of, name="metabolicProcess__subclass_of", curie=BP.curie('subclass_of'), - model_uri=BP.metabolicProcess__subclass_of, domain=None, range=Optional[Union[Union[str, MetabolicProcessCategoryId], List[Union[str, MetabolicProcessCategoryId]]]]) - -slots.metabolicProcess__category = Slot(uri=BP.category, name="metabolicProcess__category", curie=BP.curie('category'), - model_uri=BP.metabolicProcess__category, domain=None, range=Optional[Union[str, MetabolicProcessCategoryId]]) - -slots.metabolicProcess__inputs = Slot(uri=BP.inputs, name="metabolicProcess__inputs", curie=BP.curie('inputs'), - model_uri=BP.metabolicProcess__inputs, domain=None, range=Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]]) - -slots.metabolicProcess__outputs = Slot(uri=BP.outputs, name="metabolicProcess__outputs", curie=BP.curie('outputs'), - model_uri=BP.metabolicProcess__outputs, domain=None, range=Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=BP.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=BP.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=BP.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=BP.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=BP.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=BP.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=BP.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=BP.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=BP.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=BP.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=BP.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=BP.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=BP.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=BP.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=BP.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=BP.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=BP.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=BP.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=BP.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=BP.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=BP.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=BP.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=BP.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=BP.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=BP.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/metabolic_process/owl/metabolic_process.owl.ttl b/projects/metabolic_process/owl/metabolic_process.owl.ttl deleted file mode 100644 index 57f4124a0..000000000 --- a/projects/metabolic_process/owl/metabolic_process.owl.ttl +++ /dev/null @@ -1,442 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix bp: <http://w3id.org/ontogpt/metabolic-process-template> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -bp:MetabolicProcess a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MetabolicProcess" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty bp:synonyms ], - [ a owl:Restriction ; - owl:allValuesFrom bp:MetabolicProcessCategory ; - owl:onProperty bp:subclass_of ], - [ a owl:Restriction ; - owl:allValuesFrom bp:ChemicalEntity ; - owl:onProperty bp:inputs ], - [ a owl:Restriction ; - owl:allValuesFrom bp:ChemicalEntity ; - owl:onProperty bp:outputs ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass bp:MetabolicProcessCategory ; - owl:onProperty bp:category ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty bp:label ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty bp:description ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='alternative names of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a semicolon separated list of broader metabolic processes which this is a subclass of', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MetabolicProcessCategory', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'category': SlotDefinition(name='category', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MetabolicProcessCategory', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'inputs': SlotDefinition(name='inputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the inputs of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'outputs': SlotDefinition(name='outputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the outputs of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<https://w3id.org/ontogpt/metabolic_process> a owl:Ontology ; - rdfs:label "metabolic-process-template" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples> ; - linkml:classes "{'MetabolicProcess': ClassDefinition(name='MetabolicProcess', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcess', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/metabolic_process', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'metabolicProcess__label', 'metabolicProcess__description', 'metabolicProcess__synonyms', 'metabolicProcess__subclass_of', 'metabolicProcess__category', 'metabolicProcess__inputs', 'metabolicProcess__outputs'], slot_usage={}, attributes={'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='alternative names of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a semicolon separated list of broader metabolic processes which this is a subclass of', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MetabolicProcessCategory', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'category': SlotDefinition(name='category', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='MetabolicProcessCategory', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'inputs': SlotDefinition(name='inputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the inputs of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'outputs': SlotDefinition(name='outputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the outputs of the metabolic process', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='bp:MetabolicProcess', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'MetabolicProcessCategory': ClassDefinition(name='MetabolicProcessCategory', id_prefixes=['GO'], definition_uri='http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/metabolic_process', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='bp:MetabolicProcessCategory', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ChemicalEntity': ClassDefinition(name='ChemicalEntity', id_prefixes=['CHEBI'], definition_uri='http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:chebi', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/metabolic_process', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='bp:ChemicalEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/metabolic_process" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - bp:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -bp:category a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "category" ; - rdfs:range bp:MetabolicProcessCategory ; - skos:definition "the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity" . - -bp:description a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "description" ; - rdfs:range linkml:String ; - skos:definition "a textual description of the metabolic process" . - -bp:inputs a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "inputs" ; - rdfs:range bp:ChemicalEntity ; - skos:definition "the inputs of the metabolic process" . - -bp:label a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - rdfs:range linkml:String ; - skos:definition "the name of the metabolic process" . - -bp:outputs a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "outputs" ; - rdfs:range bp:ChemicalEntity ; - skos:definition "the outputs of the metabolic process" . - -bp:subclass_of a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subclass_of" ; - rdfs:range bp:MetabolicProcessCategory ; - skos:definition "a semicolon separated list of broader metabolic processes which this is a subclass of" . - -bp:synonyms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "synonyms" ; - rdfs:range linkml:String ; - skos:definition "alternative names of the metabolic process" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - bp:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -bp:ChemicalEntity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalEntity" ; - bp:annotators "sqlite:obo:chebi" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -bp:MetabolicProcessCategory a owl:Class, - linkml:ClassDefinition ; - rdfs:label "MetabolicProcessCategory" ; - bp:annotators "sqlite:obo:go" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/metabolic_process/prefixmap/metabolic_process.yaml b/projects/metabolic_process/prefixmap/metabolic_process.yaml deleted file mode 100644 index 84f0bc643..000000000 --- a/projects/metabolic_process/prefixmap/metabolic_process.yaml +++ /dev/null @@ -1,37 +0,0 @@ -{ - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "GO": "http://example.org/UNKNOWN/GO/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "bp": "http://w3id.org/ontogpt/metabolic-process-template", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/metabolic_process/protobuf/metabolic_process.proto b/projects/metabolic_process/protobuf/metabolic_process.proto deleted file mode 100644 index cd8577a6e..000000000 --- a/projects/metabolic_process/protobuf/metabolic_process.proto +++ /dev/null @@ -1,56 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message ChemicalEntity - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message MetabolicProcess - { - string id = 0 - string label = 0 - string description = 0 - repeated string synonyms = 0 - repeated metabolicProcessCategory subclassOf = 0 - metabolicProcessCategory category = 0 - repeated chemicalEntity inputs = 0 - repeated chemicalEntity outputs = 0 - } -message MetabolicProcessCategory - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/metabolic_process/shacl/metabolic_process.shacl.ttl b/projects/metabolic_process/shacl/metabolic_process.shacl.ttl deleted file mode 100644 index a914f49c1..000000000 --- a/projects/metabolic_process/shacl/metabolic_process.shacl.ttl +++ /dev/null @@ -1,234 +0,0 @@ -@prefix bp: <http://w3id.org/ontogpt/metabolic-process-template> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -bp:MetabolicProcess a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class bp:MetabolicProcessCategory ; - sh:description "a semicolon separated list of broader metabolic processes which this is a subclass of" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path bp:subclass_of ], - [ sh:description "alternative names of the metabolic process" ; - sh:order 2 ; - sh:path bp:synonyms ], - [ sh:class bp:MetabolicProcessCategory ; - sh:description "the category of metabolic process, e.g metabolic process, catabolic process, biosynthetic process, small molecule sensor activity" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path bp:category ], - [ sh:description "the name of the metabolic process" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path bp:label ], - [ sh:class bp:ChemicalEntity ; - sh:description "the outputs of the metabolic process" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path bp:outputs ], - [ sh:class bp:ChemicalEntity ; - sh:description "the inputs of the metabolic process" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path bp:inputs ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "a textual description of the metabolic process" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path bp:description ] ; - sh:targetClass bp:MetabolicProcess . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -bp:ChemicalEntity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass bp:ChemicalEntity . - -bp:MetabolicProcessCategory a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass bp:MetabolicProcessCategory . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/metabolic_process/shex/metabolic_process.shex b/projects/metabolic_process/shex/metabolic_process.shex deleted file mode 100644 index c78e8eb49..000000000 --- a/projects/metabolic_process/shex/metabolic_process.shex +++ /dev/null @@ -1,171 +0,0 @@ -BASE <http://w3id.org/ontogpt/metabolic-process-template/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity> CLOSED { - ( $<http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity> ] - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcess> CLOSED { - ( $<http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcess_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - <http://w3id.org/ontogpt/metabolic-process-templatelabel> @linkml:String ? ; - <http://w3id.org/ontogpt/metabolic-process-templatedescription> @linkml:String ? ; - <http://w3id.org/ontogpt/metabolic-process-templatesynonyms> @linkml:String * ; - <http://w3id.org/ontogpt/metabolic-process-templatesubclass_of> - @<http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory> * ; - <http://w3id.org/ontogpt/metabolic-process-templatecategory> - @<http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory> ? ; - <http://w3id.org/ontogpt/metabolic-process-templateinputs> - @<http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity> * ; - <http://w3id.org/ontogpt/metabolic-process-templateoutputs> - @<http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity> * - ) ; - rdf:type [ <http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcess> ] - ) -} - -<http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory> CLOSED { - ( $<http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory> ] - ) -} - -core:NamedEntity ( - @<http://w3id.org/ontogpt/metabolic-process-templateChemicalEntity> OR - @<http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcess> OR - @<http://w3id.org/ontogpt/metabolic-process-templateMetabolicProcessCategory> OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/metabolic_process/sqlschema/metabolic_process.sql b/projects/metabolic_process/sqlschema/metabolic_process.sql deleted file mode 100644 index 397869126..000000000 --- a/projects/metabolic_process/sqlschema/metabolic_process.sql +++ /dev/null @@ -1,71 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ChemicalEntity" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "MetabolicProcessCategory" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "MetabolicProcess" ( - id TEXT NOT NULL, - label TEXT, - description TEXT, - subclass_of TEXT, - category TEXT, - inputs TEXT, - outputs TEXT, - PRIMARY KEY (id), - FOREIGN KEY(category) REFERENCES "MetabolicProcessCategory" (id) -); - -CREATE TABLE "MetabolicProcess_synonyms" ( - backref_id TEXT, - synonyms TEXT, - PRIMARY KEY (backref_id, synonyms), - FOREIGN KEY(backref_id) REFERENCES "MetabolicProcess" (id) -); diff --git a/projects/metagenome_study/docs/AnnotatorResult.md b/projects/metagenome_study/docs/AnnotatorResult.md deleted file mode 100644 index 9dc26200c..000000000 --- a/projects/metagenome_study/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [eg:AnnotatorResult](http://w3id.org/ontogpt/environmental-metagenome/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/Any.md b/projects/metagenome_study/docs/Any.md deleted file mode 100644 index a7f410b04..000000000 --- a/projects/metagenome_study/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [eg:Any](http://w3id.org/ontogpt/environmental-metagenome/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/metagenome_study/docs/CausalRelationship.md b/projects/metagenome_study/docs/CausalRelationship.md deleted file mode 100644 index 653c41417..000000000 --- a/projects/metagenome_study/docs/CausalRelationship.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: CausalRelationship - - - - -URI: [eg:CausalRelationship](http://w3id.org/ontogpt/environmental-metagenome/CausalRelationship) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[CompoundExpression],[Variable]<effect%200..1-%20[CausalRelationship],[Variable]<cause%200..1-%20[CausalRelationship],[Study]++-%20causal_relationships%200..*>[CausalRelationship],[CompoundExpression]^-[CausalRelationship],[Study])](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[CompoundExpression],[Variable]<effect%200..1-%20[CausalRelationship],[Variable]<cause%200..1-%20[CausalRelationship],[Study]++-%20causal_relationships%200..*>[CausalRelationship],[CompoundExpression]^-[CausalRelationship],[Study]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞causal_relationships](study__causal_relationships.md)* <sub>0..\*</sub> **[CausalRelationship](CausalRelationship.md)** - -## Attributes - - -### Own - - * [➞cause](causalRelationship__cause.md) <sub>0..1</sub> - * Description: the variable that is the cause of the effect - * Range: [Variable](Variable.md) - * [➞effect](causalRelationship__effect.md) <sub>0..1</sub> - * Description: the things that is affected - * Range: [Variable](Variable.md) diff --git a/projects/metagenome_study/docs/CompoundExpression.md b/projects/metagenome_study/docs/CompoundExpression.md deleted file mode 100644 index 3d2bbfc4e..000000000 --- a/projects/metagenome_study/docs/CompoundExpression.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [eg:CompoundExpression](http://w3id.org/ontogpt/environmental-metagenome/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Measurement],[CompoundExpression]^-[Triple],[CompoundExpression]^-[Measurement],[CompoundExpression]^-[CausalRelationship],[CausalRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Measurement],[CompoundExpression]^-[Triple],[CompoundExpression]^-[Measurement],[CompoundExpression]^-[CausalRelationship],[CausalRelationship]) - -## Children - - * [CausalRelationship](CausalRelationship.md) - * [Measurement](Measurement.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/metagenome_study/docs/Environment.md b/projects/metagenome_study/docs/Environment.md deleted file mode 100644 index 180eb7508..000000000 --- a/projects/metagenome_study/docs/Environment.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Environment - - - - -URI: [eg:Environment](http://w3id.org/ontogpt/environmental-metagenome/Environment) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20environments%200..*>[Environment|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Environment],[Study])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20environments%200..*>[Environment|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Environment],[Study]) - -## Identifier prefixes - - * ENVO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞environments](study__environments.md)* <sub>0..\*</sub> **[Environment](Environment.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/EnvironmentalMaterial.md b/projects/metagenome_study/docs/EnvironmentalMaterial.md deleted file mode 100644 index dc8833c98..000000000 --- a/projects/metagenome_study/docs/EnvironmentalMaterial.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: EnvironmentalMaterial - - - - -URI: [eg:EnvironmentalMaterial](http://w3id.org/ontogpt/environmental-metagenome/EnvironmentalMaterial) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20environmental_material%200..*>[EnvironmentalMaterial|id(i):string;label(i):string%20%3F],[NamedEntity]^-[EnvironmentalMaterial],[Study])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20environmental_material%200..*>[EnvironmentalMaterial|id(i):string;label(i):string%20%3F],[NamedEntity]^-[EnvironmentalMaterial],[Study]) - -## Identifier prefixes - - * ENVO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞environmental_material](study__environmental_material.md)* <sub>0..\*</sub> **[EnvironmentalMaterial](EnvironmentalMaterial.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/ExtractionResult.md b/projects/metagenome_study/docs/ExtractionResult.md deleted file mode 100644 index 021686661..000000000 --- a/projects/metagenome_study/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [eg:ExtractionResult](http://w3id.org/ontogpt/environmental-metagenome/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/metagenome_study/docs/Location.md b/projects/metagenome_study/docs/Location.md deleted file mode 100644 index e958632fc..000000000 --- a/projects/metagenome_study/docs/Location.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Location - - - - -URI: [eg:Location](http://w3id.org/ontogpt/environmental-metagenome/Location) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20location%200..*>[Location|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Location],[Study])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Study]-%20location%200..*>[Location|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Location],[Study]) - -## Identifier prefixes - - * ENVO - * GAZ - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞location](study__location.md)* <sub>0..\*</sub> **[Location](Location.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/Measurement.md b/projects/metagenome_study/docs/Measurement.md deleted file mode 100644 index df61443ac..000000000 --- a/projects/metagenome_study/docs/Measurement.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Measurement - - - - -URI: [eg:Measurement](http://w3id.org/ontogpt/environmental-metagenome/Measurement) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[Unit]<unit%200..1-%20[Measurement|value:string%20%3F],[Study]++-%20measurements%200..*>[Measurement],[CompoundExpression]^-[Measurement],[Study],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[Unit]<unit%200..1-%20[Measurement|value:string%20%3F],[Study]++-%20measurements%200..*>[Measurement],[CompoundExpression]^-[Measurement],[Study],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞measurements](study__measurements.md)* <sub>0..\*</sub> **[Measurement](Measurement.md)** - -## Attributes - - -### Own - - * [➞value](measurement__value.md) <sub>0..1</sub> - * Description: the value of the measurement - * Range: [String](types/String.md) - * [➞unit](measurement__unit.md) <sub>0..1</sub> - * Description: the unit of the measurement - * Range: [Unit](Unit.md) diff --git a/projects/metagenome_study/docs/NamedEntity.md b/projects/metagenome_study/docs/NamedEntity.md deleted file mode 100644 index 5cd831b59..000000000 --- a/projects/metagenome_study/docs/NamedEntity.md +++ /dev/null @@ -1,41 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [eg:NamedEntity](http://w3id.org/ontogpt/environmental-metagenome/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[Unit],[Treatment],[SequencingTechnology],[RelationshipType],[Organism],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Variable],[NamedEntity]^-[Unit],[NamedEntity]^-[Treatment],[NamedEntity]^-[SequencingTechnology],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Organism],[NamedEntity]^-[Location],[NamedEntity]^-[EnvironmentalMaterial],[NamedEntity]^-[Environment],[Triple],[Location],[EnvironmentalMaterial],[Environment])](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[Unit],[Treatment],[SequencingTechnology],[RelationshipType],[Organism],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Variable],[NamedEntity]^-[Unit],[NamedEntity]^-[Treatment],[NamedEntity]^-[SequencingTechnology],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Organism],[NamedEntity]^-[Location],[NamedEntity]^-[EnvironmentalMaterial],[NamedEntity]^-[Environment],[Triple],[Location],[EnvironmentalMaterial],[Environment]) - -## Children - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [Organism](Organism.md) - * [RelationshipType](RelationshipType.md) - * [SequencingTechnology](SequencingTechnology.md) - * [Treatment](Treatment.md) - * [Unit](Unit.md) - * [Variable](Variable.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/NullDataOptions.md b/projects/metagenome_study/docs/NullDataOptions.md deleted file mode 100644 index 3765a62e3..000000000 --- a/projects/metagenome_study/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [eg:NullDataOptions](http://w3id.org/ontogpt/environmental-metagenome/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/metagenome_study/docs/Organism.md b/projects/metagenome_study/docs/Organism.md deleted file mode 100644 index d1f86c38d..000000000 --- a/projects/metagenome_study/docs/Organism.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Organism - - - - -URI: [eg:Organism](http://w3id.org/ontogpt/environmental-metagenome/Organism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Study]-%20organisms%200..*>[Organism|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Organism],[Study],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Study]-%20organisms%200..*>[Organism|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Organism],[Study],[NamedEntity]) - -## Identifier prefixes - - * NCBITaxon - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞organisms](study__organisms.md)* <sub>0..\*</sub> **[Organism](Organism.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/Publication.md b/projects/metagenome_study/docs/Publication.md deleted file mode 100644 index 69f8ed1b9..000000000 --- a/projects/metagenome_study/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [eg:Publication](http://w3id.org/ontogpt/environmental-metagenome/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/RelationshipType.md b/projects/metagenome_study/docs/RelationshipType.md deleted file mode 100644 index babb8ef3d..000000000 --- a/projects/metagenome_study/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [eg:RelationshipType](http://w3id.org/ontogpt/environmental-metagenome/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/SequencingTechnology.md b/projects/metagenome_study/docs/SequencingTechnology.md deleted file mode 100644 index fd63dd4c0..000000000 --- a/projects/metagenome_study/docs/SequencingTechnology.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: SequencingTechnology - - - - -URI: [eg:SequencingTechnology](http://w3id.org/ontogpt/environmental-metagenome/SequencingTechnology) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Study]-%20sequencing_technologies%200..1>[SequencingTechnology|id(i):string;label(i):string%20%3F],[NamedEntity]^-[SequencingTechnology],[Study],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Study]-%20sequencing_technologies%200..1>[SequencingTechnology|id(i):string;label(i):string%20%3F],[NamedEntity]^-[SequencingTechnology],[Study],[NamedEntity]) - -## Identifier prefixes - - * IDO - * EFO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞sequencing_technologies](study__sequencing_technologies.md)* <sub>0..1</sub> **[SequencingTechnology](SequencingTechnology.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/Study.md b/projects/metagenome_study/docs/Study.md deleted file mode 100644 index 9a3076adc..000000000 --- a/projects/metagenome_study/docs/Study.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Class: Study - - - - -URI: [eg:Study](http://w3id.org/ontogpt/environmental-metagenome/Study) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[Treatment],[Organism]<organisms%200..*-%20[Study],[SequencingTechnology]<sequencing_technologies%200..1-%20[Study],[EnvironmentalMaterial]<environmental_material%200..*-%20[Study],[Location]<location%200..*-%20[Study],[Measurement]<measurements%200..*-++[Study],[Treatment]<treatments%200..*-%20[Study],[Variable]<variables%200..*-%20[Study],[CausalRelationship]<causal_relationships%200..*-++[Study],[Environment]<environments%200..*-%20[Study],[SequencingTechnology],[Organism],[Measurement],[Location],[EnvironmentalMaterial],[Environment],[CausalRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[Variable],[Treatment],[Organism]<organisms%200..*-%20[Study],[SequencingTechnology]<sequencing_technologies%200..1-%20[Study],[EnvironmentalMaterial]<environmental_material%200..*-%20[Study],[Location]<location%200..*-%20[Study],[Measurement]<measurements%200..*-++[Study],[Treatment]<treatments%200..*-%20[Study],[Variable]<variables%200..*-%20[Study],[CausalRelationship]<causal_relationships%200..*-++[Study],[Environment]<environments%200..*-%20[Study],[SequencingTechnology],[Organism],[Measurement],[Location],[EnvironmentalMaterial],[Environment],[CausalRelationship]) - -## Attributes - - -### Own - - * [➞environments](study__environments.md) <sub>0..\*</sub> - * Range: [Environment](Environment.md) - * [➞causal_relationships](study__causal_relationships.md) <sub>0..\*</sub> - * Range: [CausalRelationship](CausalRelationship.md) - * [➞variables](study__variables.md) <sub>0..\*</sub> - * Range: [Variable](Variable.md) - * [➞treatments](study__treatments.md) <sub>0..\*</sub> - * Range: [Treatment](Treatment.md) - * [➞measurements](study__measurements.md) <sub>0..\*</sub> - * Range: [Measurement](Measurement.md) - * [➞location](study__location.md) <sub>0..\*</sub> - * Description: the sites at which the study was conducted - * Range: [Location](Location.md) - * [➞environmental_material](study__environmental_material.md) <sub>0..\*</sub> - * Description: the environmental material that was sampled - * Range: [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [➞sequencing_technologies](study__sequencing_technologies.md) <sub>0..1</sub> - * Range: [SequencingTechnology](SequencingTechnology.md) - * [➞organisms](study__organisms.md) <sub>0..\*</sub> - * Description: semicolon-separated list of all studied organism taxons - * Range: [Organism](Organism.md) diff --git a/projects/metagenome_study/docs/TextWithTriples.md b/projects/metagenome_study/docs/TextWithTriples.md deleted file mode 100644 index a01d0e6b2..000000000 --- a/projects/metagenome_study/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [eg:TextWithTriples](http://w3id.org/ontogpt/environmental-metagenome/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/metagenome_study/docs/Treatment.md b/projects/metagenome_study/docs/Treatment.md deleted file mode 100644 index 4031646ac..000000000 --- a/projects/metagenome_study/docs/Treatment.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Treatment - - - - -URI: [eg:Treatment](http://w3id.org/ontogpt/environmental-metagenome/Treatment) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Study]-%20treatments%200..*>[Treatment|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Treatment],[Study],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Study]-%20treatments%200..*>[Treatment|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Treatment],[Study],[NamedEntity]) - -## Identifier prefixes - - * PECO - * OBI - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞treatments](study__treatments.md)* <sub>0..\*</sub> **[Treatment](Treatment.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/Triple.md b/projects/metagenome_study/docs/Triple.md deleted file mode 100644 index 7cf604a34..000000000 --- a/projects/metagenome_study/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [eg:Triple](http://w3id.org/ontogpt/environmental-metagenome/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/metagenome_study/docs/Unit.md b/projects/metagenome_study/docs/Unit.md deleted file mode 100644 index 23f385687..000000000 --- a/projects/metagenome_study/docs/Unit.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Unit - - - - -URI: [eg:Unit](http://w3id.org/ontogpt/environmental-metagenome/Unit) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Measurement]-%20unit%200..1>[Unit|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Unit],[NamedEntity],[Measurement])](https://yuml.me/diagram/nofunky;dir:TB/class/[Measurement]-%20unit%200..1>[Unit|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Unit],[NamedEntity],[Measurement]) - -## Identifier prefixes - - * UO - * NCIT - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞unit](measurement__unit.md)* <sub>0..1</sub> **[Unit](Unit.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/Variable.md b/projects/metagenome_study/docs/Variable.md deleted file mode 100644 index f2743a207..000000000 --- a/projects/metagenome_study/docs/Variable.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Class: Variable - - - - -URI: [eg:Variable](http://w3id.org/ontogpt/environmental-metagenome/Variable) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[CausalRelationship]-%20cause%200..1>[Variable|id(i):string;label(i):string%20%3F],[CausalRelationship]-%20effect%200..1>[Variable],[Study]-%20variables%200..*>[Variable],[NamedEntity]^-[Variable],[Study],[NamedEntity],[CausalRelationship])](https://yuml.me/diagram/nofunky;dir:TB/class/[CausalRelationship]-%20cause%200..1>[Variable|id(i):string;label(i):string%20%3F],[CausalRelationship]-%20effect%200..1>[Variable],[Study]-%20variables%200..*>[Variable],[NamedEntity]^-[Variable],[Study],[NamedEntity],[CausalRelationship]) - -## Identifier prefixes - - * ENVO - * MIXS - * PATO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞cause](causalRelationship__cause.md)* <sub>0..1</sub> **[Variable](Variable.md)** - * **None** *[➞effect](causalRelationship__effect.md)* <sub>0..1</sub> **[Variable](Variable.md)** - * **None** *[➞variables](study__variables.md)* <sub>0..\*</sub> **[Variable](Variable.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/metagenome_study/docs/annotatorResult__object_id.md b/projects/metagenome_study/docs/annotatorResult__object_id.md deleted file mode 100644 index 0f0f256f6..000000000 --- a/projects/metagenome_study/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [eg:annotatorResult__object_id](http://w3id.org/ontogpt/environmental-metagenome/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/metagenome_study/docs/annotatorResult__object_text.md b/projects/metagenome_study/docs/annotatorResult__object_text.md deleted file mode 100644 index d130fdc6c..000000000 --- a/projects/metagenome_study/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [eg:annotatorResult__object_text](http://w3id.org/ontogpt/environmental-metagenome/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/metagenome_study/docs/annotatorResult__subject_text.md b/projects/metagenome_study/docs/annotatorResult__subject_text.md deleted file mode 100644 index 6a6856736..000000000 --- a/projects/metagenome_study/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [eg:annotatorResult__subject_text](http://w3id.org/ontogpt/environmental-metagenome/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/metagenome_study/docs/causalRelationship__cause.md b/projects/metagenome_study/docs/causalRelationship__cause.md deleted file mode 100644 index 911b27c2f..000000000 --- a/projects/metagenome_study/docs/causalRelationship__cause.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: cause - - -the variable that is the cause of the effect - -URI: [eg:causalRelationship__cause](http://w3id.org/ontogpt/environmental-metagenome/causalRelationship__cause) - - -## Domain and Range - -None → <sub>0..1</sub> [Variable](Variable.md) - -## Parents - - -## Children - - -## Used by - - * [CausalRelationship](CausalRelationship.md) diff --git a/projects/metagenome_study/docs/causalRelationship__effect.md b/projects/metagenome_study/docs/causalRelationship__effect.md deleted file mode 100644 index f2c270a5c..000000000 --- a/projects/metagenome_study/docs/causalRelationship__effect.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: effect - - -the things that is affected - -URI: [eg:causalRelationship__effect](http://w3id.org/ontogpt/environmental-metagenome/causalRelationship__effect) - - -## Domain and Range - -None → <sub>0..1</sub> [Variable](Variable.md) - -## Parents - - -## Children - - -## Used by - - * [CausalRelationship](CausalRelationship.md) diff --git a/projects/metagenome_study/docs/extractionResult__extracted_object.md b/projects/metagenome_study/docs/extractionResult__extracted_object.md deleted file mode 100644 index 3bce16ba9..000000000 --- a/projects/metagenome_study/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [eg:extractionResult__extracted_object](http://w3id.org/ontogpt/environmental-metagenome/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metagenome_study/docs/extractionResult__input_id.md b/projects/metagenome_study/docs/extractionResult__input_id.md deleted file mode 100644 index e7771714f..000000000 --- a/projects/metagenome_study/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [eg:extractionResult__input_id](http://w3id.org/ontogpt/environmental-metagenome/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metagenome_study/docs/extractionResult__input_text.md b/projects/metagenome_study/docs/extractionResult__input_text.md deleted file mode 100644 index 0b6ee764d..000000000 --- a/projects/metagenome_study/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [eg:extractionResult__input_text](http://w3id.org/ontogpt/environmental-metagenome/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metagenome_study/docs/extractionResult__input_title.md b/projects/metagenome_study/docs/extractionResult__input_title.md deleted file mode 100644 index 9c6974b16..000000000 --- a/projects/metagenome_study/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [eg:extractionResult__input_title](http://w3id.org/ontogpt/environmental-metagenome/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metagenome_study/docs/extractionResult__named_entities.md b/projects/metagenome_study/docs/extractionResult__named_entities.md deleted file mode 100644 index 9e1058b1d..000000000 --- a/projects/metagenome_study/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [eg:extractionResult__named_entities](http://w3id.org/ontogpt/environmental-metagenome/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metagenome_study/docs/extractionResult__prompt.md b/projects/metagenome_study/docs/extractionResult__prompt.md deleted file mode 100644 index 92f9fd7f9..000000000 --- a/projects/metagenome_study/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [eg:extractionResult__prompt](http://w3id.org/ontogpt/environmental-metagenome/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metagenome_study/docs/extractionResult__raw_completion_output.md b/projects/metagenome_study/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 8b9ce4d67..000000000 --- a/projects/metagenome_study/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [eg:extractionResult__raw_completion_output](http://w3id.org/ontogpt/environmental-metagenome/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/metagenome_study/docs/measurement__unit.md b/projects/metagenome_study/docs/measurement__unit.md deleted file mode 100644 index cc1ddbfbf..000000000 --- a/projects/metagenome_study/docs/measurement__unit.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: unit - - -the unit of the measurement - -URI: [eg:measurement__unit](http://w3id.org/ontogpt/environmental-metagenome/measurement__unit) - - -## Domain and Range - -None → <sub>0..1</sub> [Unit](Unit.md) - -## Parents - - -## Children - - -## Used by - - * [Measurement](Measurement.md) diff --git a/projects/metagenome_study/docs/measurement__value.md b/projects/metagenome_study/docs/measurement__value.md deleted file mode 100644 index 0f5c56d54..000000000 --- a/projects/metagenome_study/docs/measurement__value.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: value - - -the value of the measurement - -URI: [eg:measurement__value](http://w3id.org/ontogpt/environmental-metagenome/measurement__value) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Measurement](Measurement.md) diff --git a/projects/metagenome_study/docs/metagenome_study.md b/projects/metagenome_study/docs/metagenome_study.md deleted file mode 100644 index d3006b5fc..000000000 --- a/projects/metagenome_study/docs/metagenome_study.md +++ /dev/null @@ -1,127 +0,0 @@ - -# environmental-metagenome - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for Environmental Metagenome Studies - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [CausalRelationship](CausalRelationship.md) - * [Measurement](Measurement.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [Organism](Organism.md) - * [RelationshipType](RelationshipType.md) - * [SequencingTechnology](SequencingTechnology.md) - * [Treatment](Treatment.md) - * [Unit](Unit.md) - * [Variable](Variable.md) - * [Publication](Publication.md) - * [Study](Study.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞cause](causalRelationship__cause.md) - the variable that is the cause of the effect - * [➞effect](causalRelationship__effect.md) - the things that is affected - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞unit](measurement__unit.md) - the unit of the measurement - * [➞value](measurement__value.md) - the value of the measurement - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞causal_relationships](study__causal_relationships.md) - * [➞environmental_material](study__environmental_material.md) - the environmental material that was sampled - * [➞environments](study__environments.md) - * [➞location](study__location.md) - the sites at which the study was conducted - * [➞measurements](study__measurements.md) - * [➞organisms](study__organisms.md) - semicolon-separated list of all studied organism taxons - * [➞sequencing_technologies](study__sequencing_technologies.md) - * [➞treatments](study__treatments.md) - * [➞variables](study__variables.md) - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/metagenome_study/docs/namedEntity__id.md b/projects/metagenome_study/docs/namedEntity__id.md deleted file mode 100644 index e286fa5da..000000000 --- a/projects/metagenome_study/docs/namedEntity__id.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [eg:namedEntity__id](http://w3id.org/ontogpt/environmental-metagenome/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [NamedEntity](NamedEntity.md) - * [Organism](Organism.md) - * [RelationshipType](RelationshipType.md) - * [SequencingTechnology](SequencingTechnology.md) - * [Treatment](Treatment.md) - * [Unit](Unit.md) - * [Variable](Variable.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/metagenome_study/docs/namedEntity__label.md b/projects/metagenome_study/docs/namedEntity__label.md deleted file mode 100644 index 91f1700d0..000000000 --- a/projects/metagenome_study/docs/namedEntity__label.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [eg:namedEntity__label](http://w3id.org/ontogpt/environmental-metagenome/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Environment](Environment.md) - * [EnvironmentalMaterial](EnvironmentalMaterial.md) - * [Location](Location.md) - * [NamedEntity](NamedEntity.md) - * [Organism](Organism.md) - * [RelationshipType](RelationshipType.md) - * [SequencingTechnology](SequencingTechnology.md) - * [Treatment](Treatment.md) - * [Unit](Unit.md) - * [Variable](Variable.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/metagenome_study/docs/publication__abstract.md b/projects/metagenome_study/docs/publication__abstract.md deleted file mode 100644 index ea3b03594..000000000 --- a/projects/metagenome_study/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [eg:publication__abstract](http://w3id.org/ontogpt/environmental-metagenome/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metagenome_study/docs/publication__combined_text.md b/projects/metagenome_study/docs/publication__combined_text.md deleted file mode 100644 index 3a3660515..000000000 --- a/projects/metagenome_study/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [eg:publication__combined_text](http://w3id.org/ontogpt/environmental-metagenome/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metagenome_study/docs/publication__full_text.md b/projects/metagenome_study/docs/publication__full_text.md deleted file mode 100644 index 851f27ec7..000000000 --- a/projects/metagenome_study/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [eg:publication__full_text](http://w3id.org/ontogpt/environmental-metagenome/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metagenome_study/docs/publication__id.md b/projects/metagenome_study/docs/publication__id.md deleted file mode 100644 index 4510a8bb1..000000000 --- a/projects/metagenome_study/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [eg:publication__id](http://w3id.org/ontogpt/environmental-metagenome/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metagenome_study/docs/publication__title.md b/projects/metagenome_study/docs/publication__title.md deleted file mode 100644 index 454b784fe..000000000 --- a/projects/metagenome_study/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [eg:publication__title](http://w3id.org/ontogpt/environmental-metagenome/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/metagenome_study/docs/study__causal_relationships.md b/projects/metagenome_study/docs/study__causal_relationships.md deleted file mode 100644 index 445f65367..000000000 --- a/projects/metagenome_study/docs/study__causal_relationships.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: causal_relationships - - - - -URI: [eg:study__causal_relationships](http://w3id.org/ontogpt/environmental-metagenome/study__causal_relationships) - - -## Domain and Range - -None → <sub>0..\*</sub> [CausalRelationship](CausalRelationship.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/study__environmental_material.md b/projects/metagenome_study/docs/study__environmental_material.md deleted file mode 100644 index 74ada8ff9..000000000 --- a/projects/metagenome_study/docs/study__environmental_material.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: environmental_material - - -the environmental material that was sampled - -URI: [eg:study__environmental_material](http://w3id.org/ontogpt/environmental-metagenome/study__environmental_material) - - -## Domain and Range - -None → <sub>0..\*</sub> [EnvironmentalMaterial](EnvironmentalMaterial.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/study__environments.md b/projects/metagenome_study/docs/study__environments.md deleted file mode 100644 index 647846758..000000000 --- a/projects/metagenome_study/docs/study__environments.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: environments - - - - -URI: [eg:study__environments](http://w3id.org/ontogpt/environmental-metagenome/study__environments) - - -## Domain and Range - -None → <sub>0..\*</sub> [Environment](Environment.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/study__location.md b/projects/metagenome_study/docs/study__location.md deleted file mode 100644 index f0b5d7a61..000000000 --- a/projects/metagenome_study/docs/study__location.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: location - - -the sites at which the study was conducted - -URI: [eg:study__location](http://w3id.org/ontogpt/environmental-metagenome/study__location) - - -## Domain and Range - -None → <sub>0..\*</sub> [Location](Location.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/study__measurements.md b/projects/metagenome_study/docs/study__measurements.md deleted file mode 100644 index 4d04c0d93..000000000 --- a/projects/metagenome_study/docs/study__measurements.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: measurements - - - - -URI: [eg:study__measurements](http://w3id.org/ontogpt/environmental-metagenome/study__measurements) - - -## Domain and Range - -None → <sub>0..\*</sub> [Measurement](Measurement.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/study__organisms.md b/projects/metagenome_study/docs/study__organisms.md deleted file mode 100644 index 1ce915868..000000000 --- a/projects/metagenome_study/docs/study__organisms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: organisms - - -semicolon-separated list of all studied organism taxons - -URI: [eg:study__organisms](http://w3id.org/ontogpt/environmental-metagenome/study__organisms) - - -## Domain and Range - -None → <sub>0..\*</sub> [Organism](Organism.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/study__sequencing_technologies.md b/projects/metagenome_study/docs/study__sequencing_technologies.md deleted file mode 100644 index 27bdef22a..000000000 --- a/projects/metagenome_study/docs/study__sequencing_technologies.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: sequencing_technologies - - - - -URI: [eg:study__sequencing_technologies](http://w3id.org/ontogpt/environmental-metagenome/study__sequencing_technologies) - - -## Domain and Range - -None → <sub>0..1</sub> [SequencingTechnology](SequencingTechnology.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/study__treatments.md b/projects/metagenome_study/docs/study__treatments.md deleted file mode 100644 index e33275db8..000000000 --- a/projects/metagenome_study/docs/study__treatments.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatments - - - - -URI: [eg:study__treatments](http://w3id.org/ontogpt/environmental-metagenome/study__treatments) - - -## Domain and Range - -None → <sub>0..\*</sub> [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/study__variables.md b/projects/metagenome_study/docs/study__variables.md deleted file mode 100644 index 33f78519b..000000000 --- a/projects/metagenome_study/docs/study__variables.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: variables - - - - -URI: [eg:study__variables](http://w3id.org/ontogpt/environmental-metagenome/study__variables) - - -## Domain and Range - -None → <sub>0..\*</sub> [Variable](Variable.md) - -## Parents - - -## Children - - -## Used by - - * [Study](Study.md) diff --git a/projects/metagenome_study/docs/textWithTriples__publication.md b/projects/metagenome_study/docs/textWithTriples__publication.md deleted file mode 100644 index 6e8a399ac..000000000 --- a/projects/metagenome_study/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [eg:textWithTriples__publication](http://w3id.org/ontogpt/environmental-metagenome/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/metagenome_study/docs/textWithTriples__triples.md b/projects/metagenome_study/docs/textWithTriples__triples.md deleted file mode 100644 index ed815e562..000000000 --- a/projects/metagenome_study/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [eg:textWithTriples__triples](http://w3id.org/ontogpt/environmental-metagenome/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/metagenome_study/docs/triple__object.md b/projects/metagenome_study/docs/triple__object.md deleted file mode 100644 index a619f13a0..000000000 --- a/projects/metagenome_study/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [eg:triple__object](http://w3id.org/ontogpt/environmental-metagenome/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metagenome_study/docs/triple__object_qualifier.md b/projects/metagenome_study/docs/triple__object_qualifier.md deleted file mode 100644 index aa5e45562..000000000 --- a/projects/metagenome_study/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [eg:triple__object_qualifier](http://w3id.org/ontogpt/environmental-metagenome/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metagenome_study/docs/triple__predicate.md b/projects/metagenome_study/docs/triple__predicate.md deleted file mode 100644 index c9ae7609a..000000000 --- a/projects/metagenome_study/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [eg:triple__predicate](http://w3id.org/ontogpt/environmental-metagenome/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metagenome_study/docs/triple__qualifier.md b/projects/metagenome_study/docs/triple__qualifier.md deleted file mode 100644 index 3acc8ce50..000000000 --- a/projects/metagenome_study/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [eg:triple__qualifier](http://w3id.org/ontogpt/environmental-metagenome/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metagenome_study/docs/triple__subject.md b/projects/metagenome_study/docs/triple__subject.md deleted file mode 100644 index 29f69ea83..000000000 --- a/projects/metagenome_study/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [eg:triple__subject](http://w3id.org/ontogpt/environmental-metagenome/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metagenome_study/docs/triple__subject_qualifier.md b/projects/metagenome_study/docs/triple__subject_qualifier.md deleted file mode 100644 index 882b9d5e4..000000000 --- a/projects/metagenome_study/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [eg:triple__subject_qualifier](http://w3id.org/ontogpt/environmental-metagenome/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/metagenome_study/docs/types/Boolean.md b/projects/metagenome_study/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/metagenome_study/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/metagenome_study/docs/types/Curie.md b/projects/metagenome_study/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/metagenome_study/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/metagenome_study/docs/types/Date.md b/projects/metagenome_study/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/metagenome_study/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/metagenome_study/docs/types/DateOrDatetime.md b/projects/metagenome_study/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/metagenome_study/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/metagenome_study/docs/types/Datetime.md b/projects/metagenome_study/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/metagenome_study/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/metagenome_study/docs/types/Decimal.md b/projects/metagenome_study/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/metagenome_study/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/metagenome_study/docs/types/Double.md b/projects/metagenome_study/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/metagenome_study/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/metagenome_study/docs/types/Float.md b/projects/metagenome_study/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/metagenome_study/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/metagenome_study/docs/types/Integer.md b/projects/metagenome_study/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/metagenome_study/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/metagenome_study/docs/types/Jsonpath.md b/projects/metagenome_study/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/metagenome_study/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/metagenome_study/docs/types/Jsonpointer.md b/projects/metagenome_study/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/metagenome_study/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/metagenome_study/docs/types/Ncname.md b/projects/metagenome_study/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/metagenome_study/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/metagenome_study/docs/types/Nodeidentifier.md b/projects/metagenome_study/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/metagenome_study/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/metagenome_study/docs/types/Objectidentifier.md b/projects/metagenome_study/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/metagenome_study/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/metagenome_study/docs/types/Sparqlpath.md b/projects/metagenome_study/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/metagenome_study/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/metagenome_study/docs/types/String.md b/projects/metagenome_study/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/metagenome_study/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/metagenome_study/docs/types/Time.md b/projects/metagenome_study/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/metagenome_study/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/metagenome_study/docs/types/Uri.md b/projects/metagenome_study/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/metagenome_study/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/metagenome_study/docs/types/Uriorcurie.md b/projects/metagenome_study/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/metagenome_study/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/metagenome_study/excel/metagenome_study.xlsx b/projects/metagenome_study/excel/metagenome_study.xlsx deleted file mode 100644 index 4b57ab418dee02ecaee09f0e0f2134753c35a4bf..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 12583 zcmeHNWmJ{xwqA61H%NDPcXvp4cb9aEbR&(FfPhGYNOyOKfC7R_NylB{+1o7_&)q-n 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objectText: String - } - -type Any - { - } - -type CausalRelationship - { - cause: Variable - effect: Variable - } - -interface CompoundExpression - { - } - -type Environment - { - id: String! - label: String - } - -type EnvironmentalMaterial - { - id: String! - label: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Location - { - id: String! - label: String - } - -type Measurement - { - value: String - unit: Unit - } - -interface NamedEntity - { - id: String! - label: String - } - -type Organism - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type SequencingTechnology - { - id: String! - label: String - } - -type Study - { - environments: [Environment] - causalRelationships: [CausalRelationship] - variables: [Variable] - treatments: [Treatment] - measurements: [Measurement] - location: [Location] - environmentalMaterial: [EnvironmentalMaterial] - sequencingTechnologies: SequencingTechnology - organisms: [Organism] - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -type Treatment - { - id: String! - label: String - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - -type Unit - { - id: String! - label: String - } - -type Variable - { - id: String! - label: String - } - diff --git a/projects/metagenome_study/jsonld/metagenome_study.context.jsonld b/projects/metagenome_study/jsonld/metagenome_study.context.jsonld deleted file mode 100644 index 4c7981d7a..000000000 --- a/projects/metagenome_study/jsonld/metagenome_study.context.jsonld +++ /dev/null @@ -1,177 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:55:00", - "source": "metagenome_study.yaml" - }, - "@context": { - "EFO": "http://example.org/UNKNOWN/EFO/", - "ENVO": "http://example.org/UNKNOWN/ENVO/", - "GAZ": "http://example.org/UNKNOWN/GAZ/", - "IDO": "http://example.org/UNKNOWN/IDO/", - "MIXS": "http://example.org/UNKNOWN/MIXS/", - "NCBITaxon": "http://example.org/UNKNOWN/NCBITaxon/", - "NCIT": { - "@id": "http://purl.obolibrary.org/obo/NCIT_", - "@prefix": true - }, - "OBI": "http://example.org/UNKNOWN/OBI/", - "PATO": "http://example.org/UNKNOWN/PATO/", - "PECO": "http://example.org/UNKNOWN/PECO/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "UO": "http://example.org/UNKNOWN/UO/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "eg": "http://w3id.org/ontogpt/environmental-metagenome/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/environmental-metagenome/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "cause": { - "@type": "@id" - }, - "effect": { - "@type": "@id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "unit": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "causal_relationships": { - "@type": "@id" - }, - "environmental_material": { - "@type": "@id" - }, - "environments": { - "@type": "@id" - }, - "location": { - "@type": "@id" - }, - "measurements": { - "@type": "@id" - }, - "organisms": { - "@type": "@id" - }, - "sequencing_technologies": { - "@type": "@id" - }, - "treatments": { - "@type": "@id" - }, - "variables": { - "@type": "@id" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/metagenome_study/jsonld/metagenome_study.jsonld b/projects/metagenome_study/jsonld/metagenome_study.jsonld deleted file mode 100644 index a964918f1..000000000 --- a/projects/metagenome_study/jsonld/metagenome_study.jsonld +++ /dev/null @@ -1,1576 +0,0 @@ -{ - "name": "environmental-metagenome", - "description": "A template for Environmental Metagenome Studies", - "title": "Environmental Metagenome Template", - "id": "http://w3id.org/ontogpt/metagenome", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "eg", - "prefix_reference": "http://w3id.org/ontogpt/environmental-metagenome/" - } - ], - "default_prefix": "eg", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "study__environments", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental systems or biomes in which the study was conducted", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/environments", - "multivalued": true, - "alias": "environments", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Environment", - "@type": "SlotDefinition" - }, - { - "name": "study__causal_relationships", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/causal_relationships", - "multivalued": true, - "alias": "causal_relationships", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "CausalRelationship", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "study__variables", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental variables which are studies. E.g. temperature, pH, salinity", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/variables", - "multivalued": true, - "alias": "variables", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Variable", - "@type": "SlotDefinition" - }, - { - "name": "study__treatments", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of treatments that are applied", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/treatments", - "multivalued": true, - "alias": "treatments", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "study__measurements", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of value-measurement pairs", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/measurements", - "multivalued": true, - "alias": "measurements", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Measurement", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "study__location", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of sites at which the study was conducted", - "@type": "Annotation" - } - ], - "description": "the sites at which the study was conducted", - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/location", - "multivalued": true, - "alias": "location", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Location", - "@type": "SlotDefinition" - }, - { - "name": "study__environmental_material", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental materials", - "@type": "Annotation" - } - ], - "description": "the environmental material that was sampled", - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/environmental_material", - "multivalued": true, - "alias": "environmental_material", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "EnvironmentalMaterial", - "@type": "SlotDefinition" - }, - { - "name": "study__sequencing_technologies", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of sequencing technologies used in the project", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/sequencing_technologies", - "alias": "sequencing_technologies", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "SequencingTechnology", - "@type": "SlotDefinition" - }, - { - "name": "study__organisms", - "description": "semicolon-separated list of all studied organism taxons", - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/organisms", - "multivalued": true, - "alias": "organisms", - "owner": "Study", - "domain_of": [ - "Study" - ], - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "measurement__value", - "description": "the value of the measurement", - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/value", - "alias": "value", - "owner": "Measurement", - "domain_of": [ - "Measurement" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "measurement__unit", - "description": "the unit of the measurement", - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/unit", - "alias": "unit", - "owner": "Measurement", - "domain_of": [ - "Measurement" - ], - "range": "Unit", - "@type": "SlotDefinition" - }, - { - "name": "causalRelationship__cause", - "description": "the variable that is the cause of the effect", - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/cause", - "alias": "cause", - "owner": "CausalRelationship", - "domain_of": [ - "CausalRelationship" - ], - "range": "Variable", - "@type": "SlotDefinition" - }, - { - "name": "causalRelationship__effect", - "description": "the things that is affected", - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slot_uri": "http://w3id.org/ontogpt/environmental-metagenome/effect", - "alias": "effect", - "owner": "CausalRelationship", - "domain_of": [ - "CausalRelationship" - ], - "range": "Variable", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Study", - "definition_uri": "http://w3id.org/ontogpt/environmental-metagenome/Study", - "from_schema": "http://w3id.org/ontogpt/metagenome", - "slots": [ - "study__environments", - "study__causal_relationships", - "study__variables", - "study__treatments", - "study__measurements", - "study__location", - "study__environmental_material", - "study__sequencing_technologies", - "study__organisms" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "environments", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental systems or biomes in which the study was conducted", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "Environment", - "@type": "SlotDefinition" - }, - { - "name": "causal_relationships", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "CausalRelationship", - "@type": "SlotDefinition" - }, - { - "name": "variables", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental variables which are studies. E.g. temperature, pH, salinity", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "Variable", - "@type": "SlotDefinition" - }, - { - "name": "treatments", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of treatments that are applied", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "measurements", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of value-measurement pairs", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "Measurement", - "@type": "SlotDefinition" - }, - { - "name": "location", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of sites at which the study was conducted", - "@type": "Annotation" - } - ], - "description": "the sites at which the study was conducted", - "multivalued": true, - "range": "Location", - "@type": "SlotDefinition" - }, - { - "name": "environmental_material", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of environmental materials", - "@type": "Annotation" - } - ], - "description": "the environmental material that was sampled", - "multivalued": true, - "range": "EnvironmentalMaterial", - "@type": "SlotDefinition" - }, - { - "name": "sequencing_technologies", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of sequencing technologies used in the project", - "@type": "Annotation" - } - ], - "range": "SequencingTechnology", - "@type": "SlotDefinition" - }, - { - "name": "organisms", - "description": "semicolon-separated list of all studied organism taxons", - "multivalued": true, - "range": "Organism", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/environmental-metagenome/Study", - "@type": "ClassDefinition" - }, - { - "name": "Location", - "id_prefixes": [ - "ENVO", - "GAZ" - ], - "definition_uri": 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- "class_uri": "http://w3id.org/ontogpt/environmental-metagenome/Variable", - "@type": "ClassDefinition" - }, - { - "name": "Unit", - "id_prefixes": [ - "UO", - "NCIT" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metagenome/Unit", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:uo, bioportal:ncit", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metagenome/Unit", - "@type": "ClassDefinition" - }, - { - "name": "Measurement", - "definition_uri": "http://w3id.org/ontogpt/environmental-metagenome/Measurement", - "from_schema": "http://w3id.org/ontogpt/metagenome", - "is_a": "CompoundExpression", - "slots": [ - "measurement__value", - "measurement__unit" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "value", - "description": "the value of the 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"ClassDefinition" - }, - { - "name": "SequencingTechnology", - "id_prefixes": [ - "IDO", - "EFO" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metagenome/SequencingTechnology", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:obi, sqlite:obo:efo, bioportal:bero", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metagenome/SequencingTechnology", - "@type": "ClassDefinition" - }, - { - "name": "Treatment", - "id_prefixes": [ - "PECO", - "OBI" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metagenome/Treatment", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:peco, sqlite:obo:obi, bioportal:bero", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metagenome/Treatment", - "@type": "ClassDefinition" - }, - { - "name": "Organism", - "id_prefixes": [ - "NCBITaxon" - ], - "definition_uri": "http://w3id.org/ontogpt/environmental-metagenome/Organism", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:ncbitaxon, gilda:", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/metagenome", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/environmental-metagenome/Organism", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "metagenome_study.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 3910, - "generation_date": "2023-08-07T10:55:01", - "@type": "SchemaDefinition", - "@context": [ - "projects/metagenome_study/jsonld/metagenome_study.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/environmental-metagenome/" - } - ] -} diff --git a/projects/metagenome_study/jsonschema/metagenome_study.schema.json b/projects/metagenome_study/jsonschema/metagenome_study.schema.json deleted file mode 100644 index f38bd53fc..000000000 --- a/projects/metagenome_study/jsonschema/metagenome_study.schema.json +++ /dev/null @@ -1,387 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "CausalRelationship": { - "additionalProperties": false, - "description": "", - "properties": { - "cause": { - "description": "the variable that is the cause of the effect", - "type": "string" - }, - "effect": { - "description": "the things that is affected", - "type": "string" - } - }, - "title": "CausalRelationship", - "type": "object" - }, - "Environment": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Environment", - "type": "object" - }, - "EnvironmentalMaterial": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "EnvironmentalMaterial", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Location": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Location", - "type": "object" - }, - "Measurement": { - "additionalProperties": false, - "description": "", - "properties": { - "unit": { - "description": "the unit of the measurement", - "type": "string" - }, - "value": { - "description": "the value of the measurement", - "type": "string" - } - }, - "title": "Measurement", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Organism": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Organism", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "SequencingTechnology": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "SequencingTechnology", - "type": "object" - }, - "Study": { - "additionalProperties": false, - "description": "", - "properties": { - "causal_relationships": { - "items": { - "$ref": "#/$defs/CausalRelationship" - }, - "type": "array" - }, - "environmental_material": { - "description": "the environmental material that was sampled", - "items": { - "type": "string" - }, - "type": "array" - }, - "environments": { - "items": { - "type": "string" - }, - "type": "array" - }, - "location": { - "description": "the sites at which the study was conducted", - "items": { - "type": "string" - }, - "type": "array" - }, - "measurements": { - "items": { - "$ref": "#/$defs/Measurement" - }, - "type": "array" - }, - "organisms": { - "description": "semicolon-separated list of all studied organism taxons", - "items": { - "type": "string" - }, - "type": "array" - }, - "sequencing_technologies": { - "type": "string" - }, - "treatments": { - "items": { - "type": "string" - }, - "type": "array" - }, - "variables": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "Study", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Treatment": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Treatment", - "type": "object" - }, - "Unit": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Unit", - "type": "object" - }, - "Variable": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Variable", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/metagenome", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "environmental-metagenome", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/metagenome_study/metagenome_study.py b/projects/metagenome_study/metagenome_study.py deleted file mode 100644 index 27425570e..000000000 --- a/projects/metagenome_study/metagenome_study.py +++ /dev/null @@ -1,706 +0,0 @@ -# Auto generated from metagenome_study.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:55:11 -# Schema: environmental-metagenome -# -# id: http://w3id.org/ontogpt/metagenome -# description: A template for Environmental Metagenome Studies -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -EFO = CurieNamespace('EFO', 'http://example.org/UNKNOWN/EFO/') -ENVO = CurieNamespace('ENVO', 'http://example.org/UNKNOWN/ENVO/') -GAZ = CurieNamespace('GAZ', 'http://example.org/UNKNOWN/GAZ/') -IDO = CurieNamespace('IDO', 'http://example.org/UNKNOWN/IDO/') -MIXS = CurieNamespace('MIXS', 'http://example.org/UNKNOWN/MIXS/') -NCBITAXON = CurieNamespace('NCBITaxon', 'http://example.org/UNKNOWN/NCBITaxon/') -NCIT = CurieNamespace('NCIT', 'http://purl.obolibrary.org/obo/NCIT_') -OBI = CurieNamespace('OBI', 'http://example.org/UNKNOWN/OBI/') -PATO = CurieNamespace('PATO', 'http://example.org/UNKNOWN/PATO/') -PECO = CurieNamespace('PECO', 'http://example.org/UNKNOWN/PECO/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -UO = CurieNamespace('UO', 'http://example.org/UNKNOWN/UO/') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -EG = CurieNamespace('eg', 'http://w3id.org/ontogpt/environmental-metagenome/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = EG - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class LocationId(NamedEntityId): - pass - - -class EnvironmentalMaterialId(NamedEntityId): - pass - - -class EnvironmentId(NamedEntityId): - pass - - -class VariableId(NamedEntityId): - pass - - -class UnitId(NamedEntityId): - pass - - -class SequencingTechnologyId(NamedEntityId): - pass - - -class TreatmentId(NamedEntityId): - pass - - -class OrganismId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class Study(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.Study - class_class_curie: ClassVar[str] = "eg:Study" - class_name: ClassVar[str] = "Study" - class_model_uri: ClassVar[URIRef] = EG.Study - - environments: Optional[Union[Union[str, EnvironmentId], List[Union[str, EnvironmentId]]]] = empty_list() - causal_relationships: Optional[Union[Union[dict, "CausalRelationship"], List[Union[dict, "CausalRelationship"]]]] = empty_list() - variables: Optional[Union[Union[str, VariableId], List[Union[str, VariableId]]]] = empty_list() - treatments: Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]] = empty_list() - measurements: Optional[Union[Union[dict, "Measurement"], List[Union[dict, "Measurement"]]]] = empty_list() - location: Optional[Union[Union[str, LocationId], List[Union[str, LocationId]]]] = empty_list() - environmental_material: Optional[Union[Union[str, EnvironmentalMaterialId], List[Union[str, EnvironmentalMaterialId]]]] = empty_list() - sequencing_technologies: Optional[Union[str, SequencingTechnologyId]] = None - organisms: Optional[Union[Union[str, OrganismId], List[Union[str, OrganismId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.environments, list): - self.environments = [self.environments] if self.environments is not None else [] - self.environments = [v if isinstance(v, EnvironmentId) else EnvironmentId(v) for v in self.environments] - - if not isinstance(self.causal_relationships, list): - self.causal_relationships = [self.causal_relationships] if self.causal_relationships is not None else [] - self.causal_relationships = [v if isinstance(v, CausalRelationship) else CausalRelationship(**as_dict(v)) for v in self.causal_relationships] - - if not isinstance(self.variables, list): - self.variables = [self.variables] if self.variables is not None else [] - self.variables = [v if isinstance(v, VariableId) else VariableId(v) for v in self.variables] - - if not isinstance(self.treatments, list): - self.treatments = [self.treatments] if self.treatments is not None else [] - self.treatments = [v if isinstance(v, TreatmentId) else TreatmentId(v) for v in self.treatments] - - if not isinstance(self.measurements, list): - self.measurements = [self.measurements] if self.measurements is not None else [] - self.measurements = [v if isinstance(v, Measurement) else Measurement(**as_dict(v)) for v in self.measurements] - - if not isinstance(self.location, list): - self.location = [self.location] if self.location is not None else [] - self.location = [v if isinstance(v, LocationId) else LocationId(v) for v in self.location] - - if not isinstance(self.environmental_material, list): - self.environmental_material = [self.environmental_material] if self.environmental_material is not None else [] - self.environmental_material = [v if isinstance(v, EnvironmentalMaterialId) else EnvironmentalMaterialId(v) for v in self.environmental_material] - - if self.sequencing_technologies is not None and not isinstance(self.sequencing_technologies, SequencingTechnologyId): - self.sequencing_technologies = SequencingTechnologyId(self.sequencing_technologies) - - if not isinstance(self.organisms, list): - self.organisms = [self.organisms] if self.organisms is not None else [] - self.organisms = [v if isinstance(v, OrganismId) else OrganismId(v) for v in self.organisms] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = EG.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = EG.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Location(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.Location - class_class_curie: ClassVar[str] = "eg:Location" - class_name: ClassVar[str] = "Location" - class_model_uri: ClassVar[URIRef] = EG.Location - - id: Union[str, LocationId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, LocationId): - self.id = LocationId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class EnvironmentalMaterial(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.EnvironmentalMaterial - class_class_curie: ClassVar[str] = "eg:EnvironmentalMaterial" - class_name: ClassVar[str] = "EnvironmentalMaterial" - class_model_uri: ClassVar[URIRef] = EG.EnvironmentalMaterial - - id: Union[str, EnvironmentalMaterialId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EnvironmentalMaterialId): - self.id = EnvironmentalMaterialId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Environment(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.Environment - class_class_curie: ClassVar[str] = "eg:Environment" - class_name: ClassVar[str] = "Environment" - class_model_uri: ClassVar[URIRef] = EG.Environment - - id: Union[str, EnvironmentId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EnvironmentId): - self.id = EnvironmentId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Variable(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.Variable - class_class_curie: ClassVar[str] = "eg:Variable" - class_name: ClassVar[str] = "Variable" - class_model_uri: ClassVar[URIRef] = EG.Variable - - id: Union[str, VariableId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, VariableId): - self.id = VariableId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Unit(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.Unit - class_class_curie: ClassVar[str] = "eg:Unit" - class_name: ClassVar[str] = "Unit" - class_model_uri: ClassVar[URIRef] = EG.Unit - - id: Union[str, UnitId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, UnitId): - self.id = UnitId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class SequencingTechnology(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.SequencingTechnology - class_class_curie: ClassVar[str] = "eg:SequencingTechnology" - class_name: ClassVar[str] = "SequencingTechnology" - class_model_uri: ClassVar[URIRef] = EG.SequencingTechnology - - id: Union[str, SequencingTechnologyId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, SequencingTechnologyId): - self.id = SequencingTechnologyId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Treatment(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.Treatment - class_class_curie: ClassVar[str] = "eg:Treatment" - class_name: ClassVar[str] = "Treatment" - class_model_uri: ClassVar[URIRef] = EG.Treatment - - id: Union[str, TreatmentId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, TreatmentId): - self.id = TreatmentId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Organism(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.Organism - class_class_curie: ClassVar[str] = "eg:Organism" - class_name: ClassVar[str] = "Organism" - class_model_uri: ClassVar[URIRef] = EG.Organism - - id: Union[str, OrganismId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OrganismId): - self.id = OrganismId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = EG.CompoundExpression - - -@dataclass -class Measurement(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.Measurement - class_class_curie: ClassVar[str] = "eg:Measurement" - class_name: ClassVar[str] = "Measurement" - class_model_uri: ClassVar[URIRef] = EG.Measurement - - value: Optional[str] = None - unit: Optional[Union[str, UnitId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.value is not None and not isinstance(self.value, str): - self.value = str(self.value) - - if self.unit is not None and not isinstance(self.unit, UnitId): - self.unit = UnitId(self.unit) - - super().__post_init__(**kwargs) - - -@dataclass -class CausalRelationship(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = EG.CausalRelationship - class_class_curie: ClassVar[str] = "eg:CausalRelationship" - class_name: ClassVar[str] = "CausalRelationship" - class_model_uri: ClassVar[URIRef] = EG.CausalRelationship - - cause: Optional[Union[str, VariableId]] = None - effect: Optional[Union[str, VariableId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.cause is not None and not isinstance(self.cause, VariableId): - self.cause = VariableId(self.cause) - - if self.effect is not None and not isinstance(self.effect, VariableId): - self.effect = VariableId(self.effect) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = EG.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = EG.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = EG.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = EG.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = EG.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.study__environments = Slot(uri=EG.environments, name="study__environments", curie=EG.curie('environments'), - model_uri=EG.study__environments, domain=None, range=Optional[Union[Union[str, EnvironmentId], List[Union[str, EnvironmentId]]]]) - -slots.study__causal_relationships = Slot(uri=EG.causal_relationships, name="study__causal_relationships", curie=EG.curie('causal_relationships'), - model_uri=EG.study__causal_relationships, domain=None, range=Optional[Union[Union[dict, CausalRelationship], List[Union[dict, CausalRelationship]]]]) - -slots.study__variables = Slot(uri=EG.variables, name="study__variables", curie=EG.curie('variables'), - model_uri=EG.study__variables, domain=None, range=Optional[Union[Union[str, VariableId], List[Union[str, VariableId]]]]) - -slots.study__treatments = Slot(uri=EG.treatments, name="study__treatments", curie=EG.curie('treatments'), - model_uri=EG.study__treatments, domain=None, range=Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]]) - -slots.study__measurements = Slot(uri=EG.measurements, name="study__measurements", curie=EG.curie('measurements'), - model_uri=EG.study__measurements, domain=None, range=Optional[Union[Union[dict, Measurement], List[Union[dict, Measurement]]]]) - -slots.study__location = Slot(uri=EG.location, name="study__location", curie=EG.curie('location'), - model_uri=EG.study__location, domain=None, range=Optional[Union[Union[str, LocationId], List[Union[str, LocationId]]]]) - -slots.study__environmental_material = Slot(uri=EG.environmental_material, name="study__environmental_material", curie=EG.curie('environmental_material'), - model_uri=EG.study__environmental_material, domain=None, range=Optional[Union[Union[str, EnvironmentalMaterialId], List[Union[str, EnvironmentalMaterialId]]]]) - -slots.study__sequencing_technologies = Slot(uri=EG.sequencing_technologies, name="study__sequencing_technologies", curie=EG.curie('sequencing_technologies'), - model_uri=EG.study__sequencing_technologies, domain=None, range=Optional[Union[str, SequencingTechnologyId]]) - -slots.study__organisms = Slot(uri=EG.organisms, name="study__organisms", curie=EG.curie('organisms'), - model_uri=EG.study__organisms, domain=None, range=Optional[Union[Union[str, OrganismId], List[Union[str, OrganismId]]]]) - -slots.measurement__value = Slot(uri=EG.value, name="measurement__value", curie=EG.curie('value'), - model_uri=EG.measurement__value, domain=None, range=Optional[str]) - -slots.measurement__unit = Slot(uri=EG.unit, name="measurement__unit", curie=EG.curie('unit'), - model_uri=EG.measurement__unit, domain=None, range=Optional[Union[str, UnitId]]) - -slots.causalRelationship__cause = Slot(uri=EG.cause, name="causalRelationship__cause", curie=EG.curie('cause'), - model_uri=EG.causalRelationship__cause, domain=None, range=Optional[Union[str, VariableId]]) - -slots.causalRelationship__effect = Slot(uri=EG.effect, name="causalRelationship__effect", curie=EG.curie('effect'), - model_uri=EG.causalRelationship__effect, domain=None, range=Optional[Union[str, VariableId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=EG.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=EG.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=EG.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=EG.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=EG.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=EG.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=EG.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=EG.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=EG.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=EG.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=EG.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=EG.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=EG.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=EG.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=EG.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=EG.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=EG.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=EG.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=EG.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=EG.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=EG.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=EG.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=EG.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=EG.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=EG.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/metagenome_study/owl/metagenome_study.owl.ttl b/projects/metagenome_study/owl/metagenome_study.owl.ttl deleted file mode 100644 index 8d048afce..000000000 --- a/projects/metagenome_study/owl/metagenome_study.owl.ttl +++ /dev/null @@ -1,561 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix eg: <http://w3id.org/ontogpt/environmental-metagenome/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/metagenome> a owl:Ontology ; - rdfs:label "environmental-metagenome" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - eg:Study ; - linkml:classes "{'Study': ClassDefinition(name='Study', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/Study', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['study__environments', 'study__causal_relationships', 'study__variables', 'study__treatments', 'study__measurements', 'study__location', 'study__environmental_material', 'study__sequencing_technologies', 'study__organisms'], slot_usage={}, attributes={'environments': SlotDefinition(name='environments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental systems or biomes in which the study was conducted', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Environment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'causal_relationships': SlotDefinition(name='causal_relationships', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CausalRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'variables': SlotDefinition(name='variables', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental variables which are studies. E.g. temperature, pH, salinity', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatments': SlotDefinition(name='treatments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of treatments that are applied', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'measurements': SlotDefinition(name='measurements', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of value-measurement pairs', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Measurement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of sites at which the study was conducted', extensions={}, annotations={})}, description='the sites at which the study was conducted', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Location', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environmental_material': SlotDefinition(name='environmental_material', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental materials', extensions={}, annotations={})}, description='the environmental material that was sampled', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='EnvironmentalMaterial', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sequencing_technologies': SlotDefinition(name='sequencing_technologies', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of sequencing technologies used in the project', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='SequencingTechnology', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organisms': SlotDefinition(name='organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of all studied organism taxons', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='eg:Study', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Location': ClassDefinition(name='Location', id_prefixes=['ENVO', 'GAZ'], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/Location', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:gaz', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='eg:Location', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'EnvironmentalMaterial': ClassDefinition(name='EnvironmentalMaterial', id_prefixes=['ENVO'], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/EnvironmentalMaterial', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='eg:EnvironmentalMaterial', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Environment': ClassDefinition(name='Environment', id_prefixes=['ENVO'], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/Environment', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='eg:Environment', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Variable': ClassDefinition(name='Variable', id_prefixes=['ENVO', 'MIXS', 'PATO'], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/Variable', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:envo, bioportal:bero', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='eg:Variable', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Unit': ClassDefinition(name='Unit', id_prefixes=['UO', 'NCIT'], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/Unit', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:uo, bioportal:ncit', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='eg:Unit', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Measurement': ClassDefinition(name='Measurement', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/Measurement', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['measurement__value', 'measurement__unit'], slot_usage={}, attributes={'value': SlotDefinition(name='value', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the value of the measurement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'unit': SlotDefinition(name='unit', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the unit of the measurement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Unit', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='eg:Measurement', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CausalRelationship': ClassDefinition(name='CausalRelationship', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/CausalRelationship', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['causalRelationship__cause', 'causalRelationship__effect'], slot_usage={}, attributes={'cause': SlotDefinition(name='cause', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the variable that is the cause of the effect', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'effect': SlotDefinition(name='effect', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the things that is affected', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='eg:CausalRelationship', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'SequencingTechnology': ClassDefinition(name='SequencingTechnology', id_prefixes=['IDO', 'EFO'], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/SequencingTechnology', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:obi, sqlite:obo:efo, bioportal:bero', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='eg:SequencingTechnology', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Treatment': ClassDefinition(name='Treatment', id_prefixes=['PECO', 'OBI'], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/Treatment', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:peco, sqlite:obo:obi, bioportal:bero', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='eg:Treatment', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Organism': ClassDefinition(name='Organism', id_prefixes=['NCBITaxon'], definition_uri='http://w3id.org/ontogpt/environmental-metagenome/Organism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:ncbitaxon, gilda:', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/metagenome', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='eg:Organism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/metagenome" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - eg:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -eg:Study a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Study" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom eg:Organism ; - owl:onProperty eg:organisms ], - [ a owl:Restriction ; - owl:allValuesFrom eg:Measurement ; - owl:onProperty eg:measurements ], - [ a owl:Restriction ; - owl:allValuesFrom eg:Environment ; - owl:onProperty eg:environments ], - [ a owl:Restriction ; - owl:allValuesFrom eg:CausalRelationship ; - owl:onProperty eg:causal_relationships ], - [ a owl:Restriction ; - owl:allValuesFrom eg:Variable ; - owl:onProperty eg:variables ], - [ a owl:Restriction ; - owl:allValuesFrom eg:EnvironmentalMaterial ; - owl:onProperty eg:environmental_material ], - [ a owl:Restriction ; - owl:allValuesFrom eg:Location ; - owl:onProperty eg:location ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass eg:SequencingTechnology ; - owl:onProperty eg:sequencing_technologies ], - [ a owl:Restriction ; - owl:allValuesFrom eg:Treatment ; - owl:onProperty eg:treatments ] ; - linkml:attributes "{'environments': SlotDefinition(name='environments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental systems or biomes in which the study was conducted', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Environment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'causal_relationships': SlotDefinition(name='causal_relationships', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='CausalRelationship', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'variables': SlotDefinition(name='variables', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental variables which are studies. E.g. temperature, pH, salinity', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatments': SlotDefinition(name='treatments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of treatments that are applied', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'measurements': SlotDefinition(name='measurements', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of value-measurement pairs', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Measurement', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'location': SlotDefinition(name='location', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of sites at which the study was conducted', extensions={}, annotations={})}, description='the sites at which the study was conducted', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Location', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'environmental_material': SlotDefinition(name='environmental_material', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of environmental materials', extensions={}, annotations={})}, description='the environmental material that was sampled', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='EnvironmentalMaterial', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sequencing_technologies': SlotDefinition(name='sequencing_technologies', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of sequencing technologies used in the project', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='SequencingTechnology', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organisms': SlotDefinition(name='organisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of all studied organism taxons', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -eg:causal_relationships a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "causal_relationships" ; - eg:prompt "semicolon-separated list of cause-effect pairs, for example, effect of temperature on growth" ; - rdfs:range eg:CausalRelationship . - -eg:cause a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "cause" ; - rdfs:range eg:Variable ; - skos:definition "the variable that is the cause of the effect" . - -eg:effect a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "effect" ; - rdfs:range eg:Variable ; - skos:definition "the things that is affected" . - -eg:environmental_material a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "environmental_material" ; - eg:prompt "semicolon-separated list of environmental materials" ; - rdfs:range eg:EnvironmentalMaterial ; - skos:definition "the environmental material that was sampled" . - -eg:environments a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "environments" ; - eg:prompt "semicolon-separated list of environmental systems or biomes in which the study was conducted" ; - rdfs:range eg:Environment . - -eg:location a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "location" ; - eg:prompt "semicolon-separated list of sites at which the study was conducted" ; - rdfs:range eg:Location ; - skos:definition "the sites at which the study was conducted" . - -eg:measurements a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "measurements" ; - eg:prompt "semicolon-separated list of value-measurement pairs" ; - rdfs:range eg:Measurement . - -eg:organisms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "organisms" ; - rdfs:range eg:Organism ; - skos:definition "semicolon-separated list of all studied organism taxons" . - -eg:sequencing_technologies a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "sequencing_technologies" ; - eg:prompt "semicolon-separated list of sequencing technologies used in the project" ; - rdfs:range eg:SequencingTechnology . - -eg:treatments a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatments" ; - eg:prompt "semicolon-separated list of treatments that are applied" ; - rdfs:range eg:Treatment . - -eg:unit a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "unit" ; - rdfs:range eg:Unit ; - skos:definition "the unit of the measurement" . - -eg:value a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "value" ; - rdfs:range linkml:String ; - skos:definition "the value of the measurement" . - -eg:variables a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "variables" ; - eg:prompt "semicolon-separated list of environmental variables which are studies. E.g. temperature, pH, salinity" ; - rdfs:range eg:Variable . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - eg:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -eg:CausalRelationship a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CausalRelationship" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass eg:Variable ; - owl:onProperty eg:cause ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass eg:Variable ; - owl:onProperty eg:effect ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'cause': SlotDefinition(name='cause', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the variable that is the cause of the effect', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'effect': SlotDefinition(name='effect', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the things that is affected', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Variable', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -eg:Environment a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Environment" ; - eg:annotators "sqlite:obo:envo" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -eg:EnvironmentalMaterial a owl:Class, - linkml:ClassDefinition ; - rdfs:label "EnvironmentalMaterial" ; - eg:annotators "sqlite:obo:envo" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -eg:Location a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Location" ; - eg:annotators "sqlite:obo:envo, bioportal:gaz" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -eg:Measurement a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Measurement" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty eg:value ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass eg:Unit ; - owl:onProperty eg:unit ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'value': SlotDefinition(name='value', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the value of the measurement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'unit': SlotDefinition(name='unit', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the unit of the measurement', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Unit', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -eg:Organism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Organism" ; - eg:annotators "sqlite:obo:ncbitaxon, gilda:" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -eg:SequencingTechnology a owl:Class, - linkml:ClassDefinition ; - rdfs:label "SequencingTechnology" ; - eg:annotators "sqlite:obo:obi, sqlite:obo:efo, bioportal:bero" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -eg:Treatment a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Treatment" ; - eg:annotators "sqlite:obo:peco, sqlite:obo:obi, bioportal:bero" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -eg:Unit a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Unit" ; - eg:annotators "sqlite:obo:uo, bioportal:ncit" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -eg:Variable a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Variable" ; - eg:annotators "sqlite:obo:envo, bioportal:bero" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/metagenome_study/prefixmap/metagenome_study.yaml b/projects/metagenome_study/prefixmap/metagenome_study.yaml deleted file mode 100644 index 9a8b2c830..000000000 --- a/projects/metagenome_study/prefixmap/metagenome_study.yaml +++ /dev/null @@ -1,46 +0,0 @@ -{ - "EFO": "http://example.org/UNKNOWN/EFO/", - "ENVO": "http://example.org/UNKNOWN/ENVO/", - "GAZ": "http://example.org/UNKNOWN/GAZ/", - "IDO": "http://example.org/UNKNOWN/IDO/", - "MIXS": "http://example.org/UNKNOWN/MIXS/", - "NCBITaxon": "http://example.org/UNKNOWN/NCBITaxon/", - "NCIT": "http://purl.obolibrary.org/obo/NCIT_", - "OBI": "http://example.org/UNKNOWN/OBI/", - "PATO": "http://example.org/UNKNOWN/PATO/", - "PECO": "http://example.org/UNKNOWN/PECO/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "UO": "http://example.org/UNKNOWN/UO/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "eg": "http://w3id.org/ontogpt/environmental-metagenome/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/metagenome_study/protobuf/metagenome_study.proto b/projects/metagenome_study/protobuf/metagenome_study.proto deleted file mode 100644 index 21a5b3771..000000000 --- a/projects/metagenome_study/protobuf/metagenome_study.proto +++ /dev/null @@ -1,97 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message CausalRelationship - { - variable cause = 0 - variable effect = 0 - } -message Environment - { - string id = 0 - string label = 0 - } -message EnvironmentalMaterial - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Location - { - string id = 0 - string label = 0 - } -message Measurement - { - string value = 0 - unit unit = 0 - } -message Organism - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message SequencingTechnology - { - string id = 0 - string label = 0 - } -message Study - { - repeated environment environments = 0 - repeated causalRelationship causalRelationships = 0 - repeated variable variables = 0 - repeated treatment treatments = 0 - repeated measurement measurements = 0 - repeated location location = 0 - repeated environmentalMaterial environmentalMaterial = 0 - sequencingTechnology sequencingTechnologies = 0 - repeated organism organisms = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Treatment - { - string id = 0 - string label = 0 - } -message Unit - { - string id = 0 - string label = 0 - } -message Variable - { - string id = 0 - string label = 0 - } diff --git a/projects/metagenome_study/shacl/metagenome_study.shacl.ttl b/projects/metagenome_study/shacl/metagenome_study.shacl.ttl deleted file mode 100644 index c7ad1630c..000000000 --- a/projects/metagenome_study/shacl/metagenome_study.shacl.ttl +++ /dev/null @@ -1,353 +0,0 @@ -@prefix eg: <http://w3id.org/ontogpt/environmental-metagenome/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -eg:Study a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class eg:Measurement ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path eg:measurements ], - [ sh:class eg:CausalRelationship ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path eg:causal_relationships ], - [ sh:class eg:EnvironmentalMaterial ; - sh:description "the environmental material that was sampled" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path eg:environmental_material ], - [ sh:class eg:Organism ; - sh:description "semicolon-separated list of all studied organism taxons" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path eg:organisms ], - [ sh:class eg:Environment ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path eg:environments ], - [ sh:class eg:Variable ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path eg:variables ], - [ sh:class eg:SequencingTechnology ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path eg:sequencing_technologies ], - [ sh:class eg:Location ; - sh:description "the sites at which the study was conducted" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path eg:location ], - [ sh:class eg:Treatment ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path eg:treatments ] ; - sh:targetClass eg:Study . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -eg:CausalRelationship a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class eg:Variable ; - sh:description "the things that is affected" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path eg:effect ], - [ sh:class eg:Variable ; - sh:description "the variable that is the cause of the effect" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path eg:cause ] ; - sh:targetClass eg:CausalRelationship . - -eg:Environment a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass eg:Environment . - -eg:EnvironmentalMaterial a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass eg:EnvironmentalMaterial . - -eg:Location a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass eg:Location . - -eg:Measurement a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class eg:Unit ; - sh:description "the unit of the measurement" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path eg:unit ], - [ sh:description "the value of the measurement" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path eg:value ] ; - sh:targetClass eg:Measurement . - -eg:Organism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass eg:Organism . - -eg:SequencingTechnology a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass eg:SequencingTechnology . - -eg:Treatment a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass eg:Treatment . - -eg:Unit a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass eg:Unit . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -eg:Variable a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass eg:Variable . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/metagenome_study/shex/metagenome_study.shex b/projects/metagenome_study/shex/metagenome_study.shex deleted file mode 100644 index 786fb6e1c..000000000 --- a/projects/metagenome_study/shex/metagenome_study.shex +++ /dev/null @@ -1,236 +0,0 @@ -BASE <http://w3id.org/ontogpt/environmental-metagenome/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<CausalRelationship> CLOSED { - ( $<CausalRelationship_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <cause> @<Variable> ? ; - <effect> @<Variable> ? - ) ; - rdf:type [ <CausalRelationship> ] ? - ) -} - -core:CompoundExpression ( - @<CausalRelationship> OR @<Measurement> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -<Environment> CLOSED { - ( $<Environment_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Environment> ] - ) -} - -<EnvironmentalMaterial> CLOSED { - ( $<EnvironmentalMaterial_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <EnvironmentalMaterial> ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<Location> CLOSED { - ( $<Location_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Location> ] - ) -} - -<Measurement> CLOSED { - ( $<Measurement_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <value> @linkml:String ? ; - <unit> @<Unit> ? - ) ; - rdf:type [ <Measurement> ] ? - ) -} - -core:NamedEntity ( - @<Environment> OR @<EnvironmentalMaterial> OR @<Location> OR @<Organism> OR @core:RelationshipType OR @<SequencingTechnology> - OR @<Treatment> OR @<Unit> OR @<Variable> -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<Organism> CLOSED { - ( $<Organism_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Organism> ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -<SequencingTechnology> CLOSED { - ( $<SequencingTechnology_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <SequencingTechnology> ] - ) -} - -<Study> CLOSED { - ( $<Study_tes> ( <environments> @<Environment> * ; - <causal_relationships> @<CausalRelationship> * ; - <variables> @<Variable> * ; - <treatments> @<Treatment> * ; - <measurements> @<Measurement> * ; - <location> @<Location> * ; - <environmental_material> @<EnvironmentalMaterial> * ; - <sequencing_technologies> @<SequencingTechnology> ? ; - <organisms> @<Organism> * - ) ; - rdf:type [ <Study> ] ? - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -<Treatment> CLOSED { - ( $<Treatment_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Treatment> ] - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - -<Unit> CLOSED { - ( $<Unit_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Unit> ] - ) -} - -<Variable> CLOSED { - ( $<Variable_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Variable> ] - ) -} - - diff --git a/projects/metagenome_study/sqlschema/metagenome_study.sql b/projects/metagenome_study/sqlschema/metagenome_study.sql deleted file mode 100644 index 8c84a1f13..000000000 --- a/projects/metagenome_study/sqlschema/metagenome_study.sql +++ /dev/null @@ -1,117 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Environment" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "EnvironmentalMaterial" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Location" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Organism" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "SequencingTechnology" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Treatment" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Unit" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Variable" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "CausalRelationship" ( - cause TEXT, - effect TEXT, - PRIMARY KEY (cause, effect), - FOREIGN KEY(cause) REFERENCES "Variable" (id), - FOREIGN KEY(effect) REFERENCES "Variable" (id) -); - -CREATE TABLE "Measurement" ( - value TEXT, - unit TEXT, - PRIMARY KEY (value, unit), - FOREIGN KEY(unit) REFERENCES "Unit" (id) -); - -CREATE TABLE "Study" ( - environments TEXT, - causal_relationships TEXT, - variables TEXT, - treatments TEXT, - measurements TEXT, - location TEXT, - environmental_material TEXT, - sequencing_technologies TEXT, - organisms TEXT, - PRIMARY KEY (environments, causal_relationships, variables, treatments, measurements, location, environmental_material, sequencing_technologies, organisms), - FOREIGN KEY(sequencing_technologies) REFERENCES "SequencingTechnology" (id) -); diff --git a/projects/ontology_class/docs/AnnotatorResult.md b/projects/ontology_class/docs/AnnotatorResult.md deleted file mode 100644 index 4f189092b..000000000 --- a/projects/ontology_class/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [oc:AnnotatorResult](http://w3id.org/ontogpt/ontology-class-templateAnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/ontology_class/docs/Any.md b/projects/ontology_class/docs/Any.md deleted file mode 100644 index 75c20f2f8..000000000 --- a/projects/ontology_class/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [oc:Any](http://w3id.org/ontogpt/ontology-class-templateAny) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/ontology_class/docs/CompoundExpression.md b/projects/ontology_class/docs/CompoundExpression.md deleted file mode 100644 index 35fe2b15a..000000000 --- a/projects/ontology_class/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [oc:CompoundExpression](http://w3id.org/ontogpt/ontology-class-templateCompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/ontology_class/docs/ExtractionResult.md b/projects/ontology_class/docs/ExtractionResult.md deleted file mode 100644 index fe7d19bb9..000000000 --- a/projects/ontology_class/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [oc:ExtractionResult](http://w3id.org/ontogpt/ontology-class-templateExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/ontology_class/docs/LogicalDefinition.md b/projects/ontology_class/docs/LogicalDefinition.md deleted file mode 100644 index be5a7b0ae..000000000 --- a/projects/ontology_class/docs/LogicalDefinition.md +++ /dev/null @@ -1,26 +0,0 @@ - -# Class: LogicalDefinition - - - - -URI: [oc:LogicalDefinition](http://w3id.org/ontogpt/ontology-class-templateLogicalDefinition) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Relation],[OntologyClass],[OntologyClass]<differentiating_characteristic_parents%200..*-%20[LogicalDefinition],[Relation]<differentiating_characteristic_relationship%200..1-%20[LogicalDefinition],[OntologyClass]<genus%200..*-%20[LogicalDefinition],[OntologyClass]++-%20logical_definition%200..1>[LogicalDefinition])](https://yuml.me/diagram/nofunky;dir:TB/class/[Relation],[OntologyClass],[OntologyClass]<differentiating_characteristic_parents%200..*-%20[LogicalDefinition],[Relation]<differentiating_characteristic_relationship%200..1-%20[LogicalDefinition],[OntologyClass]<genus%200..*-%20[LogicalDefinition],[OntologyClass]++-%20logical_definition%200..1>[LogicalDefinition]) - -## Referenced by Class - - * **None** *[➞logical_definition](ontologyClass__logical_definition.md)* <sub>0..1</sub> **[LogicalDefinition](LogicalDefinition.md)** - -## Attributes - - -### Own - - * [➞genus](logicalDefinition__genus.md) <sub>0..\*</sub> - * Range: [OntologyClass](OntologyClass.md) - * [➞differentiating_characteristic_relationship](logicalDefinition__differentiating_characteristic_relationship.md) <sub>0..1</sub> - * Range: [Relation](Relation.md) - * [➞differentiating_characteristic_parents](logicalDefinition__differentiating_characteristic_parents.md) <sub>0..\*</sub> - * Range: [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_class/docs/NamedEntity.md b/projects/ontology_class/docs/NamedEntity.md deleted file mode 100644 index fba1cadc9..000000000 --- a/projects/ontology_class/docs/NamedEntity.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [oc:NamedEntity](http://w3id.org/ontogpt/ontology-class-templateNamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Relation],[OntologyClass],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Relation],[NamedEntity]^-[OntologyClass],[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Relation],[OntologyClass],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Relation],[NamedEntity]^-[OntologyClass],[Triple]) - -## Children - - * [OntologyClass](OntologyClass.md) - * [Relation](Relation.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ontology_class/docs/NullDataOptions.md b/projects/ontology_class/docs/NullDataOptions.md deleted file mode 100644 index 4b9a6758e..000000000 --- a/projects/ontology_class/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [oc:NullDataOptions](http://w3id.org/ontogpt/ontology-class-templateNullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/ontology_class/docs/OntologyClass.md b/projects/ontology_class/docs/OntologyClass.md deleted file mode 100644 index 2c94cf787..000000000 --- a/projects/ontology_class/docs/OntologyClass.md +++ /dev/null @@ -1,50 +0,0 @@ - -# Class: OntologyClass - - - - -URI: [oc:OntologyClass](http://w3id.org/ontogpt/ontology-class-templateOntologyClass) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[LogicalDefinition]<logical_definition%200..1-++[OntologyClass|label:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string],[OntologyClass]<subclass_of%200..*-%20[OntologyClass],[OntologyClass]<categories%200..*-%20[OntologyClass],[LogicalDefinition]-%20differentiating_characteristic_parents%200..*>[OntologyClass],[LogicalDefinition]-%20genus%200..*>[OntologyClass],[NamedEntity]^-[OntologyClass],[NamedEntity],[LogicalDefinition])](https://yuml.me/diagram/nofunky;dir:TB/class/[LogicalDefinition]<logical_definition%200..1-++[OntologyClass|label:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string],[OntologyClass]<subclass_of%200..*-%20[OntologyClass],[OntologyClass]<categories%200..*-%20[OntologyClass],[LogicalDefinition]-%20differentiating_characteristic_parents%200..*>[OntologyClass],[LogicalDefinition]-%20genus%200..*>[OntologyClass],[NamedEntity]^-[OntologyClass],[NamedEntity],[LogicalDefinition]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞differentiating_characteristic_parents](logicalDefinition__differentiating_characteristic_parents.md)* <sub>0..\*</sub> **[OntologyClass](OntologyClass.md)** - * **None** *[➞genus](logicalDefinition__genus.md)* <sub>0..\*</sub> **[OntologyClass](OntologyClass.md)** - * **None** *[➞categories](ontologyClass__categories.md)* <sub>0..\*</sub> **[OntologyClass](OntologyClass.md)** - * **None** *[➞subclass_of](ontologyClass__subclass_of.md)* <sub>0..\*</sub> **[OntologyClass](OntologyClass.md)** - -## Attributes - - -### Own - - * [➞label](ontologyClass__label.md) <sub>0..1</sub> - * Description: the name of the main entity being defined - * Range: [String](types/String.md) - * [➞description](ontologyClass__description.md) <sub>0..1</sub> - * Description: a textual description of the entity - * Range: [String](types/String.md) - * [➞synonyms](ontologyClass__synonyms.md) <sub>0..\*</sub> - * Description: alternative names of the entity - * Range: [String](types/String.md) - * [➞categories](ontologyClass__categories.md) <sub>0..\*</sub> - * Description: the categories to which this entity belongs. - * Range: [OntologyClass](OntologyClass.md) - * [➞subclass_of](ontologyClass__subclass_of.md) <sub>0..\*</sub> - * Range: [OntologyClass](OntologyClass.md) - * [➞logical_definition](ontologyClass__logical_definition.md) <sub>0..1</sub> - * Description: the necessary and sufficient conditions for this entity to be an instance of this class - * Range: [LogicalDefinition](LogicalDefinition.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) diff --git a/projects/ontology_class/docs/Publication.md b/projects/ontology_class/docs/Publication.md deleted file mode 100644 index a55c2f8cc..000000000 --- a/projects/ontology_class/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [oc:Publication](http://w3id.org/ontogpt/ontology-class-templatePublication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/ontology_class/docs/Relation.md b/projects/ontology_class/docs/Relation.md deleted file mode 100644 index d0d40a80d..000000000 --- a/projects/ontology_class/docs/Relation.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Relation - - - - -URI: [oc:Relation](http://w3id.org/ontogpt/ontology-class-templateRelation) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[LogicalDefinition]-%20differentiating_characteristic_relationship%200..1>[Relation|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Relation],[NamedEntity],[LogicalDefinition])](https://yuml.me/diagram/nofunky;dir:TB/class/[LogicalDefinition]-%20differentiating_characteristic_relationship%200..1>[Relation|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Relation],[NamedEntity],[LogicalDefinition]) - -## Identifier prefixes - - * RO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞differentiating_characteristic_relationship](logicalDefinition__differentiating_characteristic_relationship.md)* <sub>0..1</sub> **[Relation](Relation.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ontology_class/docs/RelationshipType.md b/projects/ontology_class/docs/RelationshipType.md deleted file mode 100644 index 4adecdef0..000000000 --- a/projects/ontology_class/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [oc:RelationshipType](http://w3id.org/ontogpt/ontology-class-templateRelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ontology_class/docs/TextWithTriples.md b/projects/ontology_class/docs/TextWithTriples.md deleted file mode 100644 index e94121934..000000000 --- a/projects/ontology_class/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [oc:TextWithTriples](http://w3id.org/ontogpt/ontology-class-templateTextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/ontology_class/docs/Triple.md b/projects/ontology_class/docs/Triple.md deleted file mode 100644 index 5a0ca3d43..000000000 --- a/projects/ontology_class/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [oc:Triple](http://w3id.org/ontogpt/ontology-class-templateTriple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/ontology_class/docs/annotatorResult__object_id.md b/projects/ontology_class/docs/annotatorResult__object_id.md deleted file mode 100644 index be14e5b97..000000000 --- a/projects/ontology_class/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [oc:annotatorResult__object_id](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ontology_class/docs/annotatorResult__object_text.md b/projects/ontology_class/docs/annotatorResult__object_text.md deleted file mode 100644 index fbf16b458..000000000 --- a/projects/ontology_class/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [oc:annotatorResult__object_text](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ontology_class/docs/annotatorResult__subject_text.md b/projects/ontology_class/docs/annotatorResult__subject_text.md deleted file mode 100644 index 1525bf843..000000000 --- a/projects/ontology_class/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [oc:annotatorResult__subject_text](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ontology_class/docs/extractionResult__extracted_object.md b/projects/ontology_class/docs/extractionResult__extracted_object.md deleted file mode 100644 index b1bc7ddff..000000000 --- a/projects/ontology_class/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [oc:extractionResult__extracted_object](http://w3id.org/ontogpt/ontology-class-templateextractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_class/docs/extractionResult__input_id.md b/projects/ontology_class/docs/extractionResult__input_id.md deleted file mode 100644 index 06eab71c1..000000000 --- a/projects/ontology_class/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [oc:extractionResult__input_id](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_class/docs/extractionResult__input_text.md b/projects/ontology_class/docs/extractionResult__input_text.md deleted file mode 100644 index 1dc6a7221..000000000 --- a/projects/ontology_class/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [oc:extractionResult__input_text](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_class/docs/extractionResult__input_title.md b/projects/ontology_class/docs/extractionResult__input_title.md deleted file mode 100644 index 2d7893d36..000000000 --- a/projects/ontology_class/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [oc:extractionResult__input_title](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_class/docs/extractionResult__named_entities.md b/projects/ontology_class/docs/extractionResult__named_entities.md deleted file mode 100644 index 37772a93c..000000000 --- a/projects/ontology_class/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [oc:extractionResult__named_entities](http://w3id.org/ontogpt/ontology-class-templateextractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_class/docs/extractionResult__prompt.md b/projects/ontology_class/docs/extractionResult__prompt.md deleted file mode 100644 index 8ba0ddcab..000000000 --- a/projects/ontology_class/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [oc:extractionResult__prompt](http://w3id.org/ontogpt/ontology-class-templateextractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_class/docs/extractionResult__raw_completion_output.md b/projects/ontology_class/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index ec9df2512..000000000 --- a/projects/ontology_class/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [oc:extractionResult__raw_completion_output](http://w3id.org/ontogpt/ontology-class-templateextractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_class/docs/logicalDefinition__differentiating_characteristic_parents.md b/projects/ontology_class/docs/logicalDefinition__differentiating_characteristic_parents.md deleted file mode 100644 index c973bd6c1..000000000 --- a/projects/ontology_class/docs/logicalDefinition__differentiating_characteristic_parents.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: differentiating_characteristic_parents - - - - -URI: [oc:logicalDefinition__differentiating_characteristic_parents](http://w3id.org/ontogpt/ontology-class-templatelogicalDefinition__differentiating_characteristic_parents) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyClass](OntologyClass.md) - -## Parents - - -## Children - - -## Used by - - * [LogicalDefinition](LogicalDefinition.md) diff --git a/projects/ontology_class/docs/logicalDefinition__differentiating_characteristic_relationship.md b/projects/ontology_class/docs/logicalDefinition__differentiating_characteristic_relationship.md deleted file mode 100644 index c638fdcf7..000000000 --- a/projects/ontology_class/docs/logicalDefinition__differentiating_characteristic_relationship.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: differentiating_characteristic_relationship - - - - -URI: [oc:logicalDefinition__differentiating_characteristic_relationship](http://w3id.org/ontogpt/ontology-class-templatelogicalDefinition__differentiating_characteristic_relationship) - - -## Domain and Range - -None → <sub>0..1</sub> [Relation](Relation.md) - -## Parents - - -## Children - - -## Used by - - * [LogicalDefinition](LogicalDefinition.md) diff --git a/projects/ontology_class/docs/logicalDefinition__genus.md b/projects/ontology_class/docs/logicalDefinition__genus.md deleted file mode 100644 index 07eb934cd..000000000 --- a/projects/ontology_class/docs/logicalDefinition__genus.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: genus - - - - -URI: [oc:logicalDefinition__genus](http://w3id.org/ontogpt/ontology-class-templatelogicalDefinition__genus) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyClass](OntologyClass.md) - -## Parents - - -## Children - - -## Used by - - * [LogicalDefinition](LogicalDefinition.md) diff --git a/projects/ontology_class/docs/namedEntity__id.md b/projects/ontology_class/docs/namedEntity__id.md deleted file mode 100644 index 6fad481c7..000000000 --- a/projects/ontology_class/docs/namedEntity__id.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [oc:namedEntity__id](http://w3id.org/ontogpt/ontology-class-templatenamedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [OntologyClass](OntologyClass.md) - * [Relation](Relation.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/ontology_class/docs/namedEntity__label.md b/projects/ontology_class/docs/namedEntity__label.md deleted file mode 100644 index 32c673a9d..000000000 --- a/projects/ontology_class/docs/namedEntity__label.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [oc:namedEntity__label](http://w3id.org/ontogpt/ontology-class-templatenamedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [Relation](Relation.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/ontology_class/docs/ontologyClass__categories.md b/projects/ontology_class/docs/ontologyClass__categories.md deleted file mode 100644 index 22d9e3e95..000000000 --- a/projects/ontology_class/docs/ontologyClass__categories.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: categories - - -the categories to which this entity belongs. - -URI: [oc:ontologyClass__categories](http://w3id.org/ontogpt/ontology-class-templateontologyClass__categories) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyClass](OntologyClass.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_class/docs/ontologyClass__description.md b/projects/ontology_class/docs/ontologyClass__description.md deleted file mode 100644 index 01eeb1a88..000000000 --- a/projects/ontology_class/docs/ontologyClass__description.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: description - - -a textual description of the entity - -URI: [oc:ontologyClass__description](http://w3id.org/ontogpt/ontology-class-templateontologyClass__description) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_class/docs/ontologyClass__label.md b/projects/ontology_class/docs/ontologyClass__label.md deleted file mode 100644 index d62bfa3ca..000000000 --- a/projects/ontology_class/docs/ontologyClass__label.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: label - - -the name of the main entity being defined - -URI: [oc:ontologyClass__label](http://w3id.org/ontogpt/ontology-class-templateontologyClass__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_class/docs/ontologyClass__logical_definition.md b/projects/ontology_class/docs/ontologyClass__logical_definition.md deleted file mode 100644 index d617d2a2d..000000000 --- a/projects/ontology_class/docs/ontologyClass__logical_definition.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: logical_definition - - -the necessary and sufficient conditions for this entity to be an instance of this class - -URI: [oc:ontologyClass__logical_definition](http://w3id.org/ontogpt/ontology-class-templateontologyClass__logical_definition) - - -## Domain and Range - -None → <sub>0..1</sub> [LogicalDefinition](LogicalDefinition.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_class/docs/ontologyClass__subclass_of.md b/projects/ontology_class/docs/ontologyClass__subclass_of.md deleted file mode 100644 index f648d140c..000000000 --- a/projects/ontology_class/docs/ontologyClass__subclass_of.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subclass_of - - - - -URI: [oc:ontologyClass__subclass_of](http://w3id.org/ontogpt/ontology-class-templateontologyClass__subclass_of) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyClass](OntologyClass.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_class/docs/ontologyClass__synonyms.md b/projects/ontology_class/docs/ontologyClass__synonyms.md deleted file mode 100644 index fa56183b1..000000000 --- a/projects/ontology_class/docs/ontologyClass__synonyms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: synonyms - - -alternative names of the entity - -URI: [oc:ontologyClass__synonyms](http://w3id.org/ontogpt/ontology-class-templateontologyClass__synonyms) - - -## Domain and Range - -None → <sub>0..\*</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_class/docs/ontology_class.md b/projects/ontology_class/docs/ontology_class.md deleted file mode 100644 index af1279bea..000000000 --- a/projects/ontology_class/docs/ontology_class.md +++ /dev/null @@ -1,115 +0,0 @@ - -# ontology-class - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for Ontology Classes - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [LogicalDefinition](LogicalDefinition.md) - * [NamedEntity](NamedEntity.md) - * [OntologyClass](OntologyClass.md) - * [Relation](Relation.md) - * [RelationshipType](RelationshipType.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞differentiating_characteristic_parents](logicalDefinition__differentiating_characteristic_parents.md) - * [➞differentiating_characteristic_relationship](logicalDefinition__differentiating_characteristic_relationship.md) - * [➞genus](logicalDefinition__genus.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞categories](ontologyClass__categories.md) - the categories to which this entity belongs. - * [➞description](ontologyClass__description.md) - a textual description of the entity - * [➞label](ontologyClass__label.md) - the name of the main entity being defined - * [➞logical_definition](ontologyClass__logical_definition.md) - the necessary and sufficient conditions for this entity to be an instance of this class - * [➞subclass_of](ontologyClass__subclass_of.md) - * [➞synonyms](ontologyClass__synonyms.md) - alternative names of the entity - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/ontology_class/docs/publication__abstract.md b/projects/ontology_class/docs/publication__abstract.md deleted file mode 100644 index 7e1c7ff37..000000000 --- a/projects/ontology_class/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [oc:publication__abstract](http://w3id.org/ontogpt/ontology-class-templatepublication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_class/docs/publication__combined_text.md b/projects/ontology_class/docs/publication__combined_text.md deleted file mode 100644 index de03f19fd..000000000 --- a/projects/ontology_class/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [oc:publication__combined_text](http://w3id.org/ontogpt/ontology-class-templatepublication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_class/docs/publication__full_text.md b/projects/ontology_class/docs/publication__full_text.md deleted file mode 100644 index ae02a60d4..000000000 --- a/projects/ontology_class/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [oc:publication__full_text](http://w3id.org/ontogpt/ontology-class-templatepublication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_class/docs/publication__id.md b/projects/ontology_class/docs/publication__id.md deleted file mode 100644 index 3fbcffacd..000000000 --- a/projects/ontology_class/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [oc:publication__id](http://w3id.org/ontogpt/ontology-class-templatepublication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_class/docs/publication__title.md b/projects/ontology_class/docs/publication__title.md deleted file mode 100644 index 5f9f7ed69..000000000 --- a/projects/ontology_class/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [oc:publication__title](http://w3id.org/ontogpt/ontology-class-templatepublication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_class/docs/textWithTriples__publication.md b/projects/ontology_class/docs/textWithTriples__publication.md deleted file mode 100644 index 27b0af18d..000000000 --- a/projects/ontology_class/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [oc:textWithTriples__publication](http://w3id.org/ontogpt/ontology-class-templatetextWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ontology_class/docs/textWithTriples__triples.md b/projects/ontology_class/docs/textWithTriples__triples.md deleted file mode 100644 index d3a729b64..000000000 --- a/projects/ontology_class/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [oc:textWithTriples__triples](http://w3id.org/ontogpt/ontology-class-templatetextWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ontology_class/docs/triple__object.md b/projects/ontology_class/docs/triple__object.md deleted file mode 100644 index 19c663552..000000000 --- a/projects/ontology_class/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [oc:triple__object](http://w3id.org/ontogpt/ontology-class-templatetriple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_class/docs/triple__object_qualifier.md b/projects/ontology_class/docs/triple__object_qualifier.md deleted file mode 100644 index bead5d4a5..000000000 --- a/projects/ontology_class/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [oc:triple__object_qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_class/docs/triple__predicate.md b/projects/ontology_class/docs/triple__predicate.md deleted file mode 100644 index 425642196..000000000 --- a/projects/ontology_class/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [oc:triple__predicate](http://w3id.org/ontogpt/ontology-class-templatetriple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_class/docs/triple__qualifier.md b/projects/ontology_class/docs/triple__qualifier.md deleted file mode 100644 index 9277dabfe..000000000 --- a/projects/ontology_class/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [oc:triple__qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_class/docs/triple__subject.md b/projects/ontology_class/docs/triple__subject.md deleted file mode 100644 index 89487785e..000000000 --- a/projects/ontology_class/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [oc:triple__subject](http://w3id.org/ontogpt/ontology-class-templatetriple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_class/docs/triple__subject_qualifier.md b/projects/ontology_class/docs/triple__subject_qualifier.md deleted file mode 100644 index e63c6bbd8..000000000 --- a/projects/ontology_class/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [oc:triple__subject_qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_class/docs/types/Boolean.md b/projects/ontology_class/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/ontology_class/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/ontology_class/docs/types/Curie.md b/projects/ontology_class/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/ontology_class/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/ontology_class/docs/types/Date.md b/projects/ontology_class/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/ontology_class/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/ontology_class/docs/types/DateOrDatetime.md b/projects/ontology_class/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/ontology_class/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ontology_class/docs/types/Datetime.md b/projects/ontology_class/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/ontology_class/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/ontology_class/docs/types/Decimal.md b/projects/ontology_class/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/ontology_class/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/ontology_class/docs/types/Double.md b/projects/ontology_class/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/ontology_class/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/ontology_class/docs/types/Float.md b/projects/ontology_class/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/ontology_class/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/ontology_class/docs/types/Integer.md b/projects/ontology_class/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/ontology_class/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/ontology_class/docs/types/Jsonpath.md b/projects/ontology_class/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/ontology_class/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ontology_class/docs/types/Jsonpointer.md b/projects/ontology_class/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/ontology_class/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ontology_class/docs/types/Ncname.md b/projects/ontology_class/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/ontology_class/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/ontology_class/docs/types/Nodeidentifier.md b/projects/ontology_class/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/ontology_class/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/ontology_class/docs/types/Objectidentifier.md b/projects/ontology_class/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/ontology_class/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/ontology_class/docs/types/Sparqlpath.md b/projects/ontology_class/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/ontology_class/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ontology_class/docs/types/String.md b/projects/ontology_class/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/ontology_class/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/ontology_class/docs/types/Time.md b/projects/ontology_class/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/ontology_class/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/ontology_class/docs/types/Uri.md b/projects/ontology_class/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/ontology_class/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/ontology_class/docs/types/Uriorcurie.md b/projects/ontology_class/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/ontology_class/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/ontology_class/excel/ontology_class.xlsx b/projects/ontology_class/excel/ontology_class.xlsx deleted file mode 100644 index 134f42bc19fe84cd07bf05d54fe13dd26c4a949f..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 8800 zcmeHtbx_q|*X^OZyFpUA8ziKqLpXFvHxdHUAl-;aN=buscSv^~T9EGU@2K;=zH)Wu 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@@ -1,87 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type LogicalDefinition - { - genus: [OntologyClass] - differentiatingCharacteristicRelationship: Relation - differentiatingCharacteristicParents: [OntologyClass] - } - -interface NamedEntity - { - id: String! - label: String - } - -type OntologyClass - { - id: String! - label: String - description: String - synonyms: [String] - categories: [OntologyClass] - subclassOf: [OntologyClass] - logicalDefinition: LogicalDefinition - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type Relation - { - id: String! - label: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/ontology_class/jsonld/ontology_class.context.jsonld b/projects/ontology_class/jsonld/ontology_class.context.jsonld deleted file mode 100644 index 1508d1715..000000000 --- a/projects/ontology_class/jsonld/ontology_class.context.jsonld +++ /dev/null @@ -1,148 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:55:16", - "source": "ontology_class.yaml" - }, - "@context": { - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "oc": { - "@id": "http://w3id.org/ontogpt/ontology-class-template", - "@prefix": true - }, - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/ontology-class-template", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "differentiating_characteristic_parents": { - "@type": "@id" - }, - "differentiating_characteristic_relationship": { - "@type": "@id" - }, - "genus": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "categories": { - "@type": "@id" - }, - "logical_definition": { - "@type": "@id" - }, - "subclass_of": { - "@type": "@id" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/ontology_class/jsonld/ontology_class.jsonld b/projects/ontology_class/jsonld/ontology_class.jsonld deleted file mode 100644 index 09ed16126..000000000 --- a/projects/ontology_class/jsonld/ontology_class.jsonld +++ /dev/null @@ -1,1285 +0,0 @@ -{ - "name": "ontology-class", - "description": "A template for Ontology Classes", - "title": "Ontology Class Template", - "id": "https://w3id.org/ontogpt/ontology_class", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "oc", - "prefix_reference": "http://w3id.org/ontogpt/ontology-class-template" - } - ], - "default_prefix": "oc", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "ontologyClass__label", - "description": "the name of the main entity being defined", - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatelabel", - "alias": "label", - "owner": "OntologyClass", - "domain_of": [ - "OntologyClass" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyClass__description", - "description": "a textual description of the entity", - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatedescription", - "alias": "description", - "owner": "OntologyClass", - "domain_of": [ - "OntologyClass" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyClass__synonyms", - "description": "alternative names of the entity", - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatesynonyms", - "multivalued": true, - "alias": "synonyms", - "owner": "OntologyClass", - "domain_of": [ - "OntologyClass" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyClass__categories", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of categories to which the entity belongs. These may be taken from an upper level ontology such as COB, BioLink, or UMLS semantic types.", - "@type": "Annotation" - } - ], - "description": "the categories to which this entity belongs.", - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatecategories", - "multivalued": true, - "alias": "categories", - "owner": "OntologyClass", - "domain_of": [ - "OntologyClass" - ], - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "ontologyClass__subclass_of", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of parent classes, indicating broader concepts. E.g. if the input text is \"a type of bone\", then the parent class is \"bone\"", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatesubclass_of", - "multivalued": true, - "alias": "subclass_of", - "owner": "OntologyClass", - "domain_of": [ - "OntologyClass" - ], - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "ontologyClass__logical_definition", - "annotations": [ - { - "tag": "prompt", - "value": "the necessary and sufficient conditions for this entity to be an instance of this class, written in OWL manchester syntax, e.g. bone and (part_of some 'hand')", - "@type": "Annotation" - } - ], - "description": "the necessary and sufficient conditions for this entity to be an instance of this class", - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatelogical_definition", - "alias": "logical_definition", - "owner": "OntologyClass", - "domain_of": [ - "OntologyClass" - ], - "range": "LogicalDefinition", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "logicalDefinition__genus", - "annotations": [ - { - "tag": "prompt", - "value": "in a logical definition expression, this is the parent (genus) class, e.g. bone", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templategenus", - "multivalued": true, - "alias": "genus", - "owner": "LogicalDefinition", - "domain_of": [ - "LogicalDefinition" - ], - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "logicalDefinition__differentiating_characteristic_relationship", - "annotations": [ - { - "tag": "prompt", - "value": "in a logical definition expression, this is the parent (differentiating characteristic) relationship type, e.g. part of", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatedifferentiating_characteristic_relationship", - "alias": "differentiating_characteristic_relationship", - "owner": "LogicalDefinition", - "domain_of": [ - "LogicalDefinition" - ], - "range": "Relation", - "@type": "SlotDefinition" - }, - { - "name": "logicalDefinition__differentiating_characteristic_parents", - "annotations": [ - { - "tag": "prompt", - "value": "in a logical definition expression, this the parent (differentiating characteristic) class, e.g. hand", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatedifferentiating_characteristic_parents", - "multivalued": true, - "alias": "differentiating_characteristic_parents", - "owner": "LogicalDefinition", - "domain_of": [ - "LogicalDefinition" - ], - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "OntologyClass", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyClass", - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "ontologyClass__label", - "ontologyClass__description", - "ontologyClass__synonyms", - "ontologyClass__categories", - "ontologyClass__subclass_of", - "ontologyClass__logical_definition" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "label", - "description": "the name of the main entity being defined", - "@type": "SlotDefinition" - }, - { - "name": "description", - "description": "a textual description of the entity", - "@type": "SlotDefinition" - }, - { - "name": "synonyms", - "description": "alternative names of the entity", - "multivalued": true, - "@type": "SlotDefinition" - }, - { - "name": "categories", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of categories to which the entity belongs. These may be taken from an upper level ontology such as COB, BioLink, or UMLS semantic types.", - "@type": "Annotation" - } - ], - "description": "the categories to which this entity belongs.", - "multivalued": true, - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "subclass_of", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of parent classes, indicating broader concepts. E.g. if the input text is \"a type of bone\", then the parent class is \"bone\"", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "logical_definition", - "annotations": [ - { - "tag": "prompt", - "value": "the necessary and sufficient conditions for this entity to be an instance of this class, written in OWL manchester syntax, e.g. bone and (part_of some 'hand')", - "@type": "Annotation" - } - ], - "description": "the necessary and sufficient conditions for this entity to be an instance of this class", - "range": "LogicalDefinition", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyClass", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "LogicalDefinition", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateLogicalDefinition", - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "slots": [ - "logicalDefinition__genus", - "logicalDefinition__differentiating_characteristic_relationship", - "logicalDefinition__differentiating_characteristic_parents" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "genus", - "annotations": [ - { - "tag": "prompt", - "value": "in a logical definition expression, this is the parent (genus) class, e.g. bone", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "differentiating_characteristic_relationship", - "annotations": [ - { - "tag": "prompt", - "value": "in a logical definition expression, this is the parent (differentiating characteristic) relationship type, e.g. part of", - "@type": "Annotation" - } - ], - "range": "Relation", - "@type": "SlotDefinition" - }, - { - "name": "differentiating_characteristic_parents", - "annotations": [ - { - "tag": "prompt", - "value": "in a logical definition expression, this the parent (differentiating characteristic) class, e.g. hand", - "@type": "Annotation" - } - ], - "multivalued": true, - "range": "OntologyClass", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateLogicalDefinition", - "@type": "ClassDefinition" - }, - { - "name": "Relation", - "id_prefixes": [ - "RO" - ], - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateRelation", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:ro", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/ontology_class", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateRelation", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "ontology_class.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 2686, - "generation_date": "2023-08-07T10:55:17", - "@type": "SchemaDefinition", - "@context": [ - "projects/ontology_class/jsonld/ontology_class.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/ontology-class-template" - } - ] -} diff --git a/projects/ontology_class/jsonschema/ontology_class.schema.json b/projects/ontology_class/jsonschema/ontology_class.schema.json deleted file mode 100644 index e721fe8c7..000000000 --- a/projects/ontology_class/jsonschema/ontology_class.schema.json +++ /dev/null @@ -1,271 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "LogicalDefinition": { - "additionalProperties": false, - "description": "", - "properties": { - "differentiating_characteristic_parents": { - "items": { - "type": "string" - }, - "type": "array" - }, - "differentiating_characteristic_relationship": { - "type": "string" - }, - "genus": { - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "LogicalDefinition", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "OntologyClass": { - "additionalProperties": false, - "description": "", - "properties": { - "categories": { - "description": "the categories to which this entity belongs.", - "items": { - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a textual description of the entity", - "type": "string" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "the name of the main entity being defined", - "type": "string" - }, - "logical_definition": { - "$ref": "#/$defs/LogicalDefinition", - "description": "the necessary and sufficient conditions for this entity to be an instance of this class" - }, - "subclass_of": { - "items": { - "type": "string" - }, - "type": "array" - }, - "synonyms": { - "description": "alternative names of the entity", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "id" - ], - "title": "OntologyClass", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "Relation": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Relation", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "https://w3id.org/ontogpt/ontology_class", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "categories": { - "description": "the categories to which this entity belongs.", - "items": { - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a textual description of the entity", - "type": "string" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "the name of the main entity being defined", - "type": "string" - }, - "logical_definition": { - "$ref": "#/$defs/LogicalDefinition", - "description": "the necessary and sufficient conditions for this entity to be an instance of this class" - }, - "subclass_of": { - "items": { - "type": "string" - }, - "type": "array" - }, - "synonyms": { - "description": "alternative names of the entity", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "id" - ], - "title": "ontology-class", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/ontology_class/ontology_class.py b/projects/ontology_class/ontology_class.py deleted file mode 100644 index 3129eb9d1..000000000 --- a/projects/ontology_class/ontology_class.py +++ /dev/null @@ -1,492 +0,0 @@ -# Auto generated from ontology_class.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:55:23 -# Schema: ontology-class -# -# id: https://w3id.org/ontogpt/ontology_class -# description: A template for Ontology Classes -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -OC = CurieNamespace('oc', 'http://w3id.org/ontogpt/ontology-class-template') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = OC - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class OntologyClassId(NamedEntityId): - pass - - -class RelationId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class LogicalDefinition(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.LogicalDefinition - class_class_curie: ClassVar[str] = "oc:LogicalDefinition" - class_name: ClassVar[str] = "LogicalDefinition" - class_model_uri: ClassVar[URIRef] = OC.LogicalDefinition - - genus: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() - differentiating_characteristic_relationship: Optional[Union[str, RelationId]] = None - differentiating_characteristic_parents: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.genus, list): - self.genus = [self.genus] if self.genus is not None else [] - self.genus = [v if isinstance(v, OntologyClassId) else OntologyClassId(v) for v in self.genus] - - if self.differentiating_characteristic_relationship is not None and not isinstance(self.differentiating_characteristic_relationship, RelationId): - self.differentiating_characteristic_relationship = RelationId(self.differentiating_characteristic_relationship) - - if not isinstance(self.differentiating_characteristic_parents, list): - self.differentiating_characteristic_parents = [self.differentiating_characteristic_parents] if self.differentiating_characteristic_parents is not None else [] - self.differentiating_characteristic_parents = [v if isinstance(v, OntologyClassId) else OntologyClassId(v) for v in self.differentiating_characteristic_parents] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = OC.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = OC.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class OntologyClass(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.OntologyClass - class_class_curie: ClassVar[str] = "oc:OntologyClass" - class_name: ClassVar[str] = "OntologyClass" - class_model_uri: ClassVar[URIRef] = OC.OntologyClass - - id: Union[str, OntologyClassId] = None - label: Optional[str] = None - description: Optional[str] = None - synonyms: Optional[Union[str, List[str]]] = empty_list() - categories: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() - subclass_of: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() - logical_definition: Optional[Union[dict, "LogicalDefinition"]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OntologyClassId): - self.id = OntologyClassId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.synonyms, list): - self.synonyms = [self.synonyms] if self.synonyms is not None else [] - self.synonyms = [v if isinstance(v, str) else str(v) for v in self.synonyms] - - if not isinstance(self.categories, list): - self.categories = [self.categories] if self.categories is not None else [] - self.categories = [v if isinstance(v, OntologyClassId) else OntologyClassId(v) for v in self.categories] - - if not isinstance(self.subclass_of, list): - self.subclass_of = [self.subclass_of] if self.subclass_of is not None else [] - self.subclass_of = [v if isinstance(v, OntologyClassId) else OntologyClassId(v) for v in self.subclass_of] - - if self.logical_definition is not None and not isinstance(self.logical_definition, LogicalDefinition): - self.logical_definition = LogicalDefinition(**as_dict(self.logical_definition)) - - super().__post_init__(**kwargs) - - -@dataclass -class Relation(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.Relation - class_class_curie: ClassVar[str] = "oc:Relation" - class_name: ClassVar[str] = "Relation" - class_model_uri: ClassVar[URIRef] = OC.Relation - - id: Union[str, RelationId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationId): - self.id = RelationId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = OC.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = OC.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = OC.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = OC.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = OC.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = OC.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.ontologyClass__label = Slot(uri=OC.label, name="ontologyClass__label", curie=OC.curie('label'), - model_uri=OC.ontologyClass__label, domain=None, range=Optional[str]) - -slots.ontologyClass__description = Slot(uri=OC.description, name="ontologyClass__description", curie=OC.curie('description'), - model_uri=OC.ontologyClass__description, domain=None, range=Optional[str]) - -slots.ontologyClass__synonyms = Slot(uri=OC.synonyms, name="ontologyClass__synonyms", curie=OC.curie('synonyms'), - model_uri=OC.ontologyClass__synonyms, domain=None, range=Optional[Union[str, List[str]]]) - -slots.ontologyClass__categories = Slot(uri=OC.categories, name="ontologyClass__categories", curie=OC.curie('categories'), - model_uri=OC.ontologyClass__categories, domain=None, range=Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]]) - -slots.ontologyClass__subclass_of = Slot(uri=OC.subclass_of, name="ontologyClass__subclass_of", curie=OC.curie('subclass_of'), - model_uri=OC.ontologyClass__subclass_of, domain=None, range=Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]]) - -slots.ontologyClass__logical_definition = Slot(uri=OC.logical_definition, name="ontologyClass__logical_definition", curie=OC.curie('logical_definition'), - model_uri=OC.ontologyClass__logical_definition, domain=None, range=Optional[Union[dict, LogicalDefinition]]) - -slots.logicalDefinition__genus = Slot(uri=OC.genus, name="logicalDefinition__genus", curie=OC.curie('genus'), - model_uri=OC.logicalDefinition__genus, domain=None, range=Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]]) - -slots.logicalDefinition__differentiating_characteristic_relationship = Slot(uri=OC.differentiating_characteristic_relationship, name="logicalDefinition__differentiating_characteristic_relationship", curie=OC.curie('differentiating_characteristic_relationship'), - model_uri=OC.logicalDefinition__differentiating_characteristic_relationship, domain=None, range=Optional[Union[str, RelationId]]) - -slots.logicalDefinition__differentiating_characteristic_parents = Slot(uri=OC.differentiating_characteristic_parents, name="logicalDefinition__differentiating_characteristic_parents", curie=OC.curie('differentiating_characteristic_parents'), - model_uri=OC.logicalDefinition__differentiating_characteristic_parents, domain=None, range=Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=OC.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=OC.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=OC.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=OC.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=OC.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=OC.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=OC.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=OC.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=OC.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=OC.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=OC.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=OC.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=OC.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=OC.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=OC.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=OC.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=OC.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=OC.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=OC.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=OC.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=OC.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=OC.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=OC.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=OC.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=OC.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/ontology_class/owl/ontology_class.owl.ttl b/projects/ontology_class/owl/ontology_class.owl.ttl deleted file mode 100644 index 00ee6e1e2..000000000 --- a/projects/ontology_class/owl/ontology_class.owl.ttl +++ /dev/null @@ -1,461 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix oc: <http://w3id.org/ontogpt/ontology-class-template> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<https://w3id.org/ontogpt/ontology_class> a owl:Ontology ; - rdfs:label "ontology-class" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - oc:LogicalDefinition ; - linkml:classes "{'OntologyClass': ClassDefinition(name='OntologyClass', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateOntologyClass', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_class', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'ontologyClass__label', 'ontologyClass__description', 'ontologyClass__synonyms', 'ontologyClass__categories', 'ontologyClass__subclass_of', 'ontologyClass__logical_definition'], slot_usage={}, attributes={'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the main entity being defined', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='alternative names of the entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'categories': SlotDefinition(name='categories', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of categories to which the entity belongs. These may be taken from an upper level ontology such as COB, BioLink, or UMLS semantic types.', extensions={}, annotations={})}, description='the categories to which this entity belongs.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of parent classes, indicating broader concepts. E.g. if the input text is \"a type of bone\", then the parent class is \"bone\"', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'logical_definition': SlotDefinition(name='logical_definition', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value=\"the necessary and sufficient conditions for this entity to be an instance of this class, written in OWL manchester syntax, e.g. bone and (part_of some 'hand')\", extensions={}, annotations={})}, description='the necessary and sufficient conditions for this entity to be an instance of this class', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='LogicalDefinition', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='oc:OntologyClass', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'LogicalDefinition': ClassDefinition(name='LogicalDefinition', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateLogicalDefinition', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_class', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['logicalDefinition__genus', 'logicalDefinition__differentiating_characteristic_relationship', 'logicalDefinition__differentiating_characteristic_parents'], slot_usage={}, attributes={'genus': SlotDefinition(name='genus', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='in a logical definition expression, this is the parent (genus) class, e.g. bone', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'differentiating_characteristic_relationship': SlotDefinition(name='differentiating_characteristic_relationship', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='in a logical definition expression, this is the parent (differentiating characteristic) relationship type, e.g. part of', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Relation', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'differentiating_characteristic_parents': SlotDefinition(name='differentiating_characteristic_parents', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='in a logical definition expression, this the parent (differentiating characteristic) class, e.g. hand', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='oc:LogicalDefinition', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Relation': ClassDefinition(name='Relation', id_prefixes=['RO'], definition_uri='http://w3id.org/ontogpt/ontology-class-templateRelation', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:ro', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_class', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='oc:Relation', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/ontology_class" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - oc:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -oc:categories a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "categories" ; - oc:prompt "semicolon-separated list of categories to which the entity belongs. These may be taken from an upper level ontology such as COB, BioLink, or UMLS semantic types." ; - rdfs:range oc:OntologyClass ; - skos:definition "the categories to which this entity belongs." . - -oc:description a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "description" ; - rdfs:range linkml:String ; - skos:definition "a textual description of the entity" . - -oc:differentiating_characteristic_parents a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "differentiating_characteristic_parents" ; - oc:prompt "in a logical definition expression, this the parent (differentiating characteristic) class, e.g. hand" ; - rdfs:range oc:OntologyClass . - -oc:differentiating_characteristic_relationship a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "differentiating_characteristic_relationship" ; - oc:prompt "in a logical definition expression, this is the parent (differentiating characteristic) relationship type, e.g. part of" ; - rdfs:range oc:Relation . - -oc:genus a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "genus" ; - oc:prompt "in a logical definition expression, this is the parent (genus) class, e.g. bone" ; - rdfs:range oc:OntologyClass . - -oc:label a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - rdfs:range linkml:String ; - skos:definition "the name of the main entity being defined" . - -oc:logical_definition a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "logical_definition" ; - oc:prompt "the necessary and sufficient conditions for this entity to be an instance of this class, written in OWL manchester syntax, e.g. bone and (part_of some 'hand')" ; - rdfs:range oc:LogicalDefinition ; - skos:definition "the necessary and sufficient conditions for this entity to be an instance of this class" . - -oc:subclass_of a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subclass_of" ; - oc:prompt "semicolon-separated list of parent classes, indicating broader concepts. E.g. if the input text is \"a type of bone\", then the parent class is \"bone\"" ; - rdfs:range oc:OntologyClass . - -oc:synonyms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "synonyms" ; - rdfs:range linkml:String ; - skos:definition "alternative names of the entity" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - oc:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -oc:Relation a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Relation" ; - oc:annotators "sqlite:obo:ro" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -oc:LogicalDefinition a owl:Class, - linkml:ClassDefinition ; - rdfs:label "LogicalDefinition" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass oc:Relation ; - owl:onProperty oc:differentiating_characteristic_relationship ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyClass ; - owl:onProperty oc:differentiating_characteristic_parents ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyClass ; - owl:onProperty oc:genus ] ; - linkml:attributes "{'genus': SlotDefinition(name='genus', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='in a logical definition expression, this is the parent (genus) class, e.g. bone', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'differentiating_characteristic_relationship': SlotDefinition(name='differentiating_characteristic_relationship', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='in a logical definition expression, this is the parent (differentiating characteristic) relationship type, e.g. part of', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Relation', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'differentiating_characteristic_parents': SlotDefinition(name='differentiating_characteristic_parents', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='in a logical definition expression, this the parent (differentiating characteristic) class, e.g. hand', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -oc:OntologyClass a owl:Class, - linkml:ClassDefinition ; - rdfs:label "OntologyClass" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:description ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyClass ; - owl:onProperty oc:subclass_of ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:label ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty oc:synonyms ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass oc:LogicalDefinition ; - owl:onProperty oc:logical_definition ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyClass ; - owl:onProperty oc:categories ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the main entity being defined', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='alternative names of the entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'categories': SlotDefinition(name='categories', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of categories to which the entity belongs. These may be taken from an upper level ontology such as COB, BioLink, or UMLS semantic types.', extensions={}, annotations={})}, description='the categories to which this entity belongs.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of parent classes, indicating broader concepts. E.g. if the input text is \"a type of bone\", then the parent class is \"bone\"', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'logical_definition': SlotDefinition(name='logical_definition', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value=\"the necessary and sufficient conditions for this entity to be an instance of this class, written in OWL manchester syntax, e.g. bone and (part_of some 'hand')\", extensions={}, annotations={})}, description='the necessary and sufficient conditions for this entity to be an instance of this class', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='LogicalDefinition', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/ontology_class/prefixmap/ontology_class.yaml b/projects/ontology_class/prefixmap/ontology_class.yaml deleted file mode 100644 index d7c94693b..000000000 --- a/projects/ontology_class/prefixmap/ontology_class.yaml +++ /dev/null @@ -1,35 +0,0 @@ -{ - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "oc": "http://w3id.org/ontogpt/ontology-class-template", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/ontology_class/protobuf/ontology_class.proto b/projects/ontology_class/protobuf/ontology_class.proto deleted file mode 100644 index 6a684de6e..000000000 --- a/projects/ontology_class/protobuf/ontology_class.proto +++ /dev/null @@ -1,56 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message LogicalDefinition - { - repeated ontologyClass genus = 0 - relation differentiatingCharacteristicRelationship = 0 - repeated ontologyClass differentiatingCharacteristicParents = 0 - } -message OntologyClass - { - string id = 0 - string label = 0 - string description = 0 - repeated string synonyms = 0 - repeated ontologyClass categories = 0 - repeated ontologyClass subclassOf = 0 - logicalDefinition logicalDefinition = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message Relation - { - string id = 0 - string label = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/ontology_class/shacl/ontology_class.shacl.ttl b/projects/ontology_class/shacl/ontology_class.shacl.ttl deleted file mode 100644 index d7f6620c4..000000000 --- a/projects/ontology_class/shacl/ontology_class.shacl.ttl +++ /dev/null @@ -1,232 +0,0 @@ -@prefix linkml: <https://w3id.org/linkml/> . -@prefix oc: <http://w3id.org/ontogpt/ontology-class-template> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ], - [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -oc:LogicalDefinition a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class oc:OntologyClass ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path oc:differentiating_characteristic_parents ], - [ sh:class oc:OntologyClass ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path oc:genus ], - [ sh:class oc:Relation ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path oc:differentiating_characteristic_relationship ] ; - sh:targetClass oc:LogicalDefinition . - -oc:Relation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass oc:Relation . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - -oc:OntologyClass a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class oc:LogicalDefinition ; - sh:description "the necessary and sufficient conditions for this entity to be an instance of this class" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path oc:logical_definition ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:class oc:OntologyClass ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path oc:subclass_of ], - [ sh:class oc:OntologyClass ; - sh:description "the categories to which this entity belongs." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path oc:categories ], - [ sh:description "a textual description of the entity" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path oc:description ], - [ sh:description "alternative names of the entity" ; - sh:order 2 ; - sh:path oc:synonyms ], - [ sh:description "the name of the main entity being defined" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path oc:label ] ; - sh:targetClass oc:OntologyClass . - diff --git a/projects/ontology_class/shex/ontology_class.shex b/projects/ontology_class/shex/ontology_class.shex deleted file mode 100644 index d6ebdf44a..000000000 --- a/projects/ontology_class/shex/ontology_class.shex +++ /dev/null @@ -1,173 +0,0 @@ -BASE <http://w3id.org/ontogpt/ontology-class-template/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateLogicalDefinition> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateLogicalDefinition_tes> ( - <http://w3id.org/ontogpt/ontology-class-templategenus> @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> * - ; - <http://w3id.org/ontogpt/ontology-class-templatedifferentiating_characteristic_relationship> - @<http://w3id.org/ontogpt/ontology-class-templateRelation> ? ; - <http://w3id.org/ontogpt/ontology-class-templatedifferentiating_characteristic_parents> - @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> * - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateLogicalDefinition> ] ? - ) -} - -core:NamedEntity ( - @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> OR @<http://w3id.org/ontogpt/ontology-class-templateRelation> - OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateOntologyClass_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - <http://w3id.org/ontogpt/ontology-class-templatelabel> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatedescription> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatesynonyms> @linkml:String * ; - <http://w3id.org/ontogpt/ontology-class-templatecategories> - @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> * ; - <http://w3id.org/ontogpt/ontology-class-templatesubclass_of> - @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> * ; - <http://w3id.org/ontogpt/ontology-class-templatelogical_definition> - @<http://w3id.org/ontogpt/ontology-class-templateLogicalDefinition> ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateOntologyClass> ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateRelation> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateRelation_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateRelation> ] - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/ontology_class/sqlschema/ontology_class.sql b/projects/ontology_class/sqlschema/ontology_class.sql deleted file mode 100644 index 3fbad0bd3..000000000 --- a/projects/ontology_class/sqlschema/ontology_class.sql +++ /dev/null @@ -1,71 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "OntologyClass" ( - id TEXT NOT NULL, - label TEXT, - description TEXT, - categories TEXT, - subclass_of TEXT, - logical_definition TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "Relation" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "LogicalDefinition" ( - genus TEXT, - differentiating_characteristic_relationship TEXT, - differentiating_characteristic_parents TEXT, - PRIMARY KEY (genus, differentiating_characteristic_relationship, differentiating_characteristic_parents), - FOREIGN KEY(differentiating_characteristic_relationship) REFERENCES "Relation" (id) -); - -CREATE TABLE "OntologyClass_synonyms" ( - backref_id TEXT, - synonyms TEXT, - PRIMARY KEY (backref_id, synonyms), - FOREIGN KEY(backref_id) REFERENCES "OntologyClass" (id) -); diff --git a/projects/ontology_issue/docs/AnnotatorResult.md b/projects/ontology_issue/docs/AnnotatorResult.md deleted file mode 100644 index 4f189092b..000000000 --- a/projects/ontology_issue/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [oc:AnnotatorResult](http://w3id.org/ontogpt/ontology-class-templateAnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/ontology_issue/docs/Any.md b/projects/ontology_issue/docs/Any.md deleted file mode 100644 index 75c20f2f8..000000000 --- a/projects/ontology_issue/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [oc:Any](http://w3id.org/ontogpt/ontology-class-templateAny) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/ontology_issue/docs/ChangeType.md b/projects/ontology_issue/docs/ChangeType.md deleted file mode 100644 index 3ea79df25..000000000 --- a/projects/ontology_issue/docs/ChangeType.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Enum: ChangeType - - - - -URI: [oc:ChangeType](http://w3id.org/ontogpt/ontology-class-templateChangeType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNKNOWN | | | | -| CHANGE_DEFINITION | | | | -| CHANGE_LABEL | | | | -| CHANGE_XREF | | | | -| MOVE_TERM | | | | - diff --git a/projects/ontology_issue/docs/CompoundExpression.md b/projects/ontology_issue/docs/CompoundExpression.md deleted file mode 100644 index 1e1d4dd38..000000000 --- a/projects/ontology_issue/docs/CompoundExpression.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [oc:CompoundExpression](http://w3id.org/ontogpt/ontology-class-templateCompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[OntologyProblem],[OntologyChange],[CompoundExpression]^-[Triple],[CompoundExpression]^-[OntologyProblem],[CompoundExpression]^-[OntologyChange])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[OntologyProblem],[OntologyChange],[CompoundExpression]^-[Triple],[CompoundExpression]^-[OntologyProblem],[CompoundExpression]^-[OntologyChange]) - -## Children - - * [OntologyChange](OntologyChange.md) - * [OntologyProblem](OntologyProblem.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/ontology_issue/docs/ExtractionResult.md b/projects/ontology_issue/docs/ExtractionResult.md deleted file mode 100644 index fe7d19bb9..000000000 --- a/projects/ontology_issue/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [oc:ExtractionResult](http://w3id.org/ontogpt/ontology-class-templateExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/ontology_issue/docs/NamedEntity.md b/projects/ontology_issue/docs/NamedEntity.md deleted file mode 100644 index a3f5f4d52..000000000 --- a/projects/ontology_issue/docs/NamedEntity.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [oc:NamedEntity](http://w3id.org/ontogpt/ontology-class-templateNamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[OntologyClass],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[OntologyClass],[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[OntologyClass],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[OntologyClass],[Triple]) - -## Children - - * [OntologyClass](OntologyClass.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ontology_issue/docs/NullDataOptions.md b/projects/ontology_issue/docs/NullDataOptions.md deleted file mode 100644 index 4b9a6758e..000000000 --- a/projects/ontology_issue/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [oc:NullDataOptions](http://w3id.org/ontogpt/ontology-class-templateNullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/ontology_issue/docs/OntologyChange.md b/projects/ontology_issue/docs/OntologyChange.md deleted file mode 100644 index 5797a47ff..000000000 --- a/projects/ontology_issue/docs/OntologyChange.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Class: OntologyChange - - - - -URI: [oc:OntologyChange](http://w3id.org/ontogpt/ontology-class-templateOntologyChange) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyClass],[OntologyClass]<about%200..*-%20[OntologyChange|description:string%20%3F;category:ChangeType%20%3F],[OntologyIssue]++-%20proposed_changes%200..*>[OntologyChange],[CompoundExpression]^-[OntologyChange],[OntologyIssue],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyClass],[OntologyClass]<about%200..*-%20[OntologyChange|description:string%20%3F;category:ChangeType%20%3F],[OntologyIssue]++-%20proposed_changes%200..*>[OntologyChange],[CompoundExpression]^-[OntologyChange],[OntologyIssue],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞proposed_changes](ontologyIssue__proposed_changes.md)* <sub>0..\*</sub> **[OntologyChange](OntologyChange.md)** - -## Attributes - - -### Own - - * [➞description](ontologyChange__description.md) <sub>0..1</sub> - * Description: A succinct description of the proposed change - * Range: [String](types/String.md) - * [➞category](ontologyChange__category.md) <sub>0..1</sub> - * Description: What kind of change? - * Range: [ChangeType](ChangeType.md) - * [➞about](ontologyChange__about.md) <sub>0..\*</sub> - * Description: What terms in the ontology will this change affect? - * Range: [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_issue/docs/OntologyClass.md b/projects/ontology_issue/docs/OntologyClass.md deleted file mode 100644 index 57455ae27..000000000 --- a/projects/ontology_issue/docs/OntologyClass.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: OntologyClass - - - - -URI: [oc:OntologyClass](http://w3id.org/ontogpt/ontology-class-templateOntologyClass) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyChange]-%20about%200..*>[OntologyClass|id(i):string;label(i):string%20%3F],[OntologyIssue]-%20domains%200..*>[OntologyClass],[OntologyProblem]-%20about%200..*>[OntologyClass],[NamedEntity]^-[OntologyClass],[OntologyProblem],[OntologyIssue],[OntologyChange],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyChange]-%20about%200..*>[OntologyClass|id(i):string;label(i):string%20%3F],[OntologyIssue]-%20domains%200..*>[OntologyClass],[OntologyProblem]-%20about%200..*>[OntologyClass],[NamedEntity]^-[OntologyClass],[OntologyProblem],[OntologyIssue],[OntologyChange],[NamedEntity]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞about](ontologyChange__about.md)* <sub>0..\*</sub> **[OntologyClass](OntologyClass.md)** - * **None** *[➞domains](ontologyIssue__domains.md)* <sub>0..\*</sub> **[OntologyClass](OntologyClass.md)** - * **None** *[➞about](ontologyProblem__about.md)* <sub>0..\*</sub> **[OntologyClass](OntologyClass.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ontology_issue/docs/OntologyIssue.md b/projects/ontology_issue/docs/OntologyIssue.md deleted file mode 100644 index 0bcbc9999..000000000 --- a/projects/ontology_issue/docs/OntologyIssue.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Class: OntologyIssue - - - - -URI: [oc:OntologyIssue](http://w3id.org/ontogpt/ontology-class-templateOntologyIssue) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyProblem],[OntologyChange]<proposed_changes%200..*-++[OntologyIssue|title:string%20%3F;summary:string%20%3F;status:string%20%3F],[OntologyProblem]<problem_list%200..*-++[OntologyIssue],[OntologyClass]<domains%200..*-%20[OntologyIssue],[OntologyClass],[OntologyChange])](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyProblem],[OntologyChange]<proposed_changes%200..*-++[OntologyIssue|title:string%20%3F;summary:string%20%3F;status:string%20%3F],[OntologyProblem]<problem_list%200..*-++[OntologyIssue],[OntologyClass]<domains%200..*-%20[OntologyIssue],[OntologyClass],[OntologyChange]) - -## Attributes - - -### Own - - * [➞title](ontologyIssue__title.md) <sub>0..1</sub> - * Description: the title of the issue - * Range: [String](types/String.md) - * [➞summary](ontologyIssue__summary.md) <sub>0..1</sub> - * Description: a high level summary - * Range: [String](types/String.md) - * [➞status](ontologyIssue__status.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞domains](ontologyIssue__domains.md) <sub>0..\*</sub> - * Description: What part of the ontology does this pertain to. - * Range: [OntologyClass](OntologyClass.md) - * [➞problem_list](ontologyIssue__problem_list.md) <sub>0..\*</sub> - * Description: A list of problems stated at a high level - * Range: [OntologyProblem](OntologyProblem.md) - * [➞proposed_changes](ontologyIssue__proposed_changes.md) <sub>0..\*</sub> - * Description: What part of the ontology does this pertain to. - * Range: [OntologyChange](OntologyChange.md) diff --git a/projects/ontology_issue/docs/OntologyProblem.md b/projects/ontology_issue/docs/OntologyProblem.md deleted file mode 100644 index 2d0fef019..000000000 --- a/projects/ontology_issue/docs/OntologyProblem.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: OntologyProblem - - - - -URI: [oc:OntologyProblem](http://w3id.org/ontogpt/ontology-class-templateOntologyProblem) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyClass]<about%200..*-%20[OntologyProblem|description:string%20%3F;severity:string%20%3F;category:ProblemType%20%3F],[OntologyIssue]++-%20problem_list%200..*>[OntologyProblem],[CompoundExpression]^-[OntologyProblem],[OntologyIssue],[OntologyClass],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[OntologyClass]<about%200..*-%20[OntologyProblem|description:string%20%3F;severity:string%20%3F;category:ProblemType%20%3F],[OntologyIssue]++-%20problem_list%200..*>[OntologyProblem],[CompoundExpression]^-[OntologyProblem],[OntologyIssue],[OntologyClass],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞problem_list](ontologyIssue__problem_list.md)* <sub>0..\*</sub> **[OntologyProblem](OntologyProblem.md)** - -## Attributes - - -### Own - - * [➞description](ontologyProblem__description.md) <sub>0..1</sub> - * Description: A succinct description of the problem - * Range: [String](types/String.md) - * [➞severity](ontologyProblem__severity.md) <sub>0..1</sub> - * Description: How severe is this problem? - * Range: [String](types/String.md) - * [➞category](ontologyProblem__category.md) <sub>0..1</sub> - * Description: What category does this problem fall into? - * Range: [ProblemType](ProblemType.md) - * [➞about](ontologyProblem__about.md) <sub>0..\*</sub> - * Description: What terms in the ontology is this problem about? - * Range: [OntologyClass](OntologyClass.md) diff --git a/projects/ontology_issue/docs/ProblemType.md b/projects/ontology_issue/docs/ProblemType.md deleted file mode 100644 index 7eb7d154c..000000000 --- a/projects/ontology_issue/docs/ProblemType.md +++ /dev/null @@ -1,26 +0,0 @@ - -# Enum: ProblemType - - - - -URI: [oc:ProblemType](http://w3id.org/ontogpt/ontology-class-templateProblemType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNKNOWN | | | | -| TYPO | | | | -| BAD_XREF | | | | -| MISSING_DEFINITION | | | | -| MISSING_PARENT | | | | -| BAD_RELATIONSHIP | | | | -| OTHER | | | | - diff --git a/projects/ontology_issue/docs/Publication.md b/projects/ontology_issue/docs/Publication.md deleted file mode 100644 index a55c2f8cc..000000000 --- a/projects/ontology_issue/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [oc:Publication](http://w3id.org/ontogpt/ontology-class-templatePublication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/ontology_issue/docs/RelationshipType.md b/projects/ontology_issue/docs/RelationshipType.md deleted file mode 100644 index 4adecdef0..000000000 --- a/projects/ontology_issue/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [oc:RelationshipType](http://w3id.org/ontogpt/ontology-class-templateRelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/ontology_issue/docs/TextWithTriples.md b/projects/ontology_issue/docs/TextWithTriples.md deleted file mode 100644 index e94121934..000000000 --- a/projects/ontology_issue/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [oc:TextWithTriples](http://w3id.org/ontogpt/ontology-class-templateTextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/ontology_issue/docs/Triple.md b/projects/ontology_issue/docs/Triple.md deleted file mode 100644 index 5a0ca3d43..000000000 --- a/projects/ontology_issue/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [oc:Triple](http://w3id.org/ontogpt/ontology-class-templateTriple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/ontology_issue/docs/annotatorResult__object_id.md b/projects/ontology_issue/docs/annotatorResult__object_id.md deleted file mode 100644 index be14e5b97..000000000 --- a/projects/ontology_issue/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [oc:annotatorResult__object_id](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ontology_issue/docs/annotatorResult__object_text.md b/projects/ontology_issue/docs/annotatorResult__object_text.md deleted file mode 100644 index fbf16b458..000000000 --- a/projects/ontology_issue/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [oc:annotatorResult__object_text](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ontology_issue/docs/annotatorResult__subject_text.md b/projects/ontology_issue/docs/annotatorResult__subject_text.md deleted file mode 100644 index 1525bf843..000000000 --- a/projects/ontology_issue/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [oc:annotatorResult__subject_text](http://w3id.org/ontogpt/ontology-class-templateannotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/ontology_issue/docs/extractionResult__extracted_object.md b/projects/ontology_issue/docs/extractionResult__extracted_object.md deleted file mode 100644 index b1bc7ddff..000000000 --- a/projects/ontology_issue/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [oc:extractionResult__extracted_object](http://w3id.org/ontogpt/ontology-class-templateextractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_issue/docs/extractionResult__input_id.md b/projects/ontology_issue/docs/extractionResult__input_id.md deleted file mode 100644 index 06eab71c1..000000000 --- a/projects/ontology_issue/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [oc:extractionResult__input_id](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_issue/docs/extractionResult__input_text.md b/projects/ontology_issue/docs/extractionResult__input_text.md deleted file mode 100644 index 1dc6a7221..000000000 --- a/projects/ontology_issue/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [oc:extractionResult__input_text](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_issue/docs/extractionResult__input_title.md b/projects/ontology_issue/docs/extractionResult__input_title.md deleted file mode 100644 index 2d7893d36..000000000 --- a/projects/ontology_issue/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [oc:extractionResult__input_title](http://w3id.org/ontogpt/ontology-class-templateextractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_issue/docs/extractionResult__named_entities.md b/projects/ontology_issue/docs/extractionResult__named_entities.md deleted file mode 100644 index 37772a93c..000000000 --- a/projects/ontology_issue/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [oc:extractionResult__named_entities](http://w3id.org/ontogpt/ontology-class-templateextractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_issue/docs/extractionResult__prompt.md b/projects/ontology_issue/docs/extractionResult__prompt.md deleted file mode 100644 index 8ba0ddcab..000000000 --- a/projects/ontology_issue/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [oc:extractionResult__prompt](http://w3id.org/ontogpt/ontology-class-templateextractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_issue/docs/extractionResult__raw_completion_output.md b/projects/ontology_issue/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index ec9df2512..000000000 --- a/projects/ontology_issue/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [oc:extractionResult__raw_completion_output](http://w3id.org/ontogpt/ontology-class-templateextractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/ontology_issue/docs/namedEntity__id.md b/projects/ontology_issue/docs/namedEntity__id.md deleted file mode 100644 index 4a2cd961b..000000000 --- a/projects/ontology_issue/docs/namedEntity__id.md +++ /dev/null @@ -1,31 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [oc:namedEntity__id](http://w3id.org/ontogpt/ontology-class-templatenamedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [OntologyClass](OntologyClass.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/ontology_issue/docs/namedEntity__label.md b/projects/ontology_issue/docs/namedEntity__label.md deleted file mode 100644 index 03552dc0a..000000000 --- a/projects/ontology_issue/docs/namedEntity__label.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [oc:namedEntity__label](http://w3id.org/ontogpt/ontology-class-templatenamedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [OntologyClass](OntologyClass.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/ontology_issue/docs/ontologyChange__about.md b/projects/ontology_issue/docs/ontologyChange__about.md deleted file mode 100644 index 1f9f75b60..000000000 --- a/projects/ontology_issue/docs/ontologyChange__about.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: about - - -What terms in the ontology will this change affect? - -URI: [oc:ontologyChange__about](http://w3id.org/ontogpt/ontology-class-templateontologyChange__about) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyClass](OntologyClass.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyChange](OntologyChange.md) diff --git a/projects/ontology_issue/docs/ontologyChange__category.md b/projects/ontology_issue/docs/ontologyChange__category.md deleted file mode 100644 index 677ce9bc2..000000000 --- a/projects/ontology_issue/docs/ontologyChange__category.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: category - - -What kind of change? - -URI: [oc:ontologyChange__category](http://w3id.org/ontogpt/ontology-class-templateontologyChange__category) - - -## Domain and Range - -None → <sub>0..1</sub> [ChangeType](ChangeType.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyChange](OntologyChange.md) diff --git a/projects/ontology_issue/docs/ontologyChange__description.md b/projects/ontology_issue/docs/ontologyChange__description.md deleted file mode 100644 index 8c815de49..000000000 --- a/projects/ontology_issue/docs/ontologyChange__description.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: description - - -A succinct description of the proposed change - -URI: [oc:ontologyChange__description](http://w3id.org/ontogpt/ontology-class-templateontologyChange__description) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyChange](OntologyChange.md) diff --git a/projects/ontology_issue/docs/ontologyIssue__domains.md b/projects/ontology_issue/docs/ontologyIssue__domains.md deleted file mode 100644 index ae6a2c436..000000000 --- a/projects/ontology_issue/docs/ontologyIssue__domains.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: domains - - -What part of the ontology does this pertain to. - -URI: [oc:ontologyIssue__domains](http://w3id.org/ontogpt/ontology-class-templateontologyIssue__domains) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyClass](OntologyClass.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyIssue](OntologyIssue.md) diff --git a/projects/ontology_issue/docs/ontologyIssue__problem_list.md b/projects/ontology_issue/docs/ontologyIssue__problem_list.md deleted file mode 100644 index a4b1088ab..000000000 --- a/projects/ontology_issue/docs/ontologyIssue__problem_list.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: problem_list - - -A list of problems stated at a high level - -URI: [oc:ontologyIssue__problem_list](http://w3id.org/ontogpt/ontology-class-templateontologyIssue__problem_list) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyProblem](OntologyProblem.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyIssue](OntologyIssue.md) diff --git a/projects/ontology_issue/docs/ontologyIssue__proposed_changes.md b/projects/ontology_issue/docs/ontologyIssue__proposed_changes.md deleted file mode 100644 index d74166a67..000000000 --- a/projects/ontology_issue/docs/ontologyIssue__proposed_changes.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: proposed_changes - - -What part of the ontology does this pertain to. - -URI: [oc:ontologyIssue__proposed_changes](http://w3id.org/ontogpt/ontology-class-templateontologyIssue__proposed_changes) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyChange](OntologyChange.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyIssue](OntologyIssue.md) diff --git a/projects/ontology_issue/docs/ontologyIssue__status.md b/projects/ontology_issue/docs/ontologyIssue__status.md deleted file mode 100644 index 729aa27de..000000000 --- a/projects/ontology_issue/docs/ontologyIssue__status.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: status - - - - -URI: [oc:ontologyIssue__status](http://w3id.org/ontogpt/ontology-class-templateontologyIssue__status) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyIssue](OntologyIssue.md) diff --git a/projects/ontology_issue/docs/ontologyIssue__summary.md b/projects/ontology_issue/docs/ontologyIssue__summary.md deleted file mode 100644 index d44e96302..000000000 --- a/projects/ontology_issue/docs/ontologyIssue__summary.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: summary - - -a high level summary - -URI: [oc:ontologyIssue__summary](http://w3id.org/ontogpt/ontology-class-templateontologyIssue__summary) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyIssue](OntologyIssue.md) diff --git a/projects/ontology_issue/docs/ontologyIssue__title.md b/projects/ontology_issue/docs/ontologyIssue__title.md deleted file mode 100644 index 1841d9231..000000000 --- a/projects/ontology_issue/docs/ontologyIssue__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -the title of the issue - -URI: [oc:ontologyIssue__title](http://w3id.org/ontogpt/ontology-class-templateontologyIssue__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyIssue](OntologyIssue.md) diff --git a/projects/ontology_issue/docs/ontologyProblem__about.md b/projects/ontology_issue/docs/ontologyProblem__about.md deleted file mode 100644 index d8c6d2a12..000000000 --- a/projects/ontology_issue/docs/ontologyProblem__about.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: about - - -What terms in the ontology is this problem about? - -URI: [oc:ontologyProblem__about](http://w3id.org/ontogpt/ontology-class-templateontologyProblem__about) - - -## Domain and Range - -None → <sub>0..\*</sub> [OntologyClass](OntologyClass.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyProblem](OntologyProblem.md) diff --git a/projects/ontology_issue/docs/ontologyProblem__category.md b/projects/ontology_issue/docs/ontologyProblem__category.md deleted file mode 100644 index 9d2308473..000000000 --- a/projects/ontology_issue/docs/ontologyProblem__category.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: category - - -What category does this problem fall into? - -URI: [oc:ontologyProblem__category](http://w3id.org/ontogpt/ontology-class-templateontologyProblem__category) - - -## Domain and Range - -None → <sub>0..1</sub> [ProblemType](ProblemType.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyProblem](OntologyProblem.md) diff --git a/projects/ontology_issue/docs/ontologyProblem__description.md b/projects/ontology_issue/docs/ontologyProblem__description.md deleted file mode 100644 index b85edbdf7..000000000 --- a/projects/ontology_issue/docs/ontologyProblem__description.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: description - - -A succinct description of the problem - -URI: [oc:ontologyProblem__description](http://w3id.org/ontogpt/ontology-class-templateontologyProblem__description) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyProblem](OntologyProblem.md) diff --git a/projects/ontology_issue/docs/ontologyProblem__severity.md b/projects/ontology_issue/docs/ontologyProblem__severity.md deleted file mode 100644 index 5148a03dd..000000000 --- a/projects/ontology_issue/docs/ontologyProblem__severity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: severity - - -How severe is this problem? - -URI: [oc:ontologyProblem__severity](http://w3id.org/ontogpt/ontology-class-templateontologyProblem__severity) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [OntologyProblem](OntologyProblem.md) diff --git a/projects/ontology_issue/docs/ontology_issue.md b/projects/ontology_issue/docs/ontology_issue.md deleted file mode 100644 index 8bcf333ac..000000000 --- a/projects/ontology_issue/docs/ontology_issue.md +++ /dev/null @@ -1,122 +0,0 @@ - -# ontology-issue - - -**metamodel version:** 1.7.0 - -**version:** None - - -A data model for representing the contents of a GitHub issue on an ontology tracker - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [OntologyChange](OntologyChange.md) - * [OntologyProblem](OntologyProblem.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [OntologyClass](OntologyClass.md) - * [RelationshipType](RelationshipType.md) - * [OntologyIssue](OntologyIssue.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞about](ontologyChange__about.md) - What terms in the ontology will this change affect? - * [➞category](ontologyChange__category.md) - What kind of change? - * [➞description](ontologyChange__description.md) - A succinct description of the proposed change - * [➞domains](ontologyIssue__domains.md) - What part of the ontology does this pertain to. - * [➞problem_list](ontologyIssue__problem_list.md) - A list of problems stated at a high level - * [➞proposed_changes](ontologyIssue__proposed_changes.md) - What part of the ontology does this pertain to. - * [➞status](ontologyIssue__status.md) - * [➞summary](ontologyIssue__summary.md) - a high level summary - * [➞title](ontologyIssue__title.md) - the title of the issue - * [➞about](ontologyProblem__about.md) - What terms in the ontology is this problem about? - * [➞category](ontologyProblem__category.md) - What category does this problem fall into? - * [➞description](ontologyProblem__description.md) - A succinct description of the problem - * [➞severity](ontologyProblem__severity.md) - How severe is this problem? - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [ChangeType](ChangeType.md) - * [NullDataOptions](NullDataOptions.md) - * [ProblemType](ProblemType.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/ontology_issue/docs/publication__abstract.md b/projects/ontology_issue/docs/publication__abstract.md deleted file mode 100644 index 7e1c7ff37..000000000 --- a/projects/ontology_issue/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [oc:publication__abstract](http://w3id.org/ontogpt/ontology-class-templatepublication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_issue/docs/publication__combined_text.md b/projects/ontology_issue/docs/publication__combined_text.md deleted file mode 100644 index de03f19fd..000000000 --- a/projects/ontology_issue/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [oc:publication__combined_text](http://w3id.org/ontogpt/ontology-class-templatepublication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_issue/docs/publication__full_text.md b/projects/ontology_issue/docs/publication__full_text.md deleted file mode 100644 index ae02a60d4..000000000 --- a/projects/ontology_issue/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [oc:publication__full_text](http://w3id.org/ontogpt/ontology-class-templatepublication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_issue/docs/publication__id.md b/projects/ontology_issue/docs/publication__id.md deleted file mode 100644 index 3fbcffacd..000000000 --- a/projects/ontology_issue/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [oc:publication__id](http://w3id.org/ontogpt/ontology-class-templatepublication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_issue/docs/publication__title.md b/projects/ontology_issue/docs/publication__title.md deleted file mode 100644 index 5f9f7ed69..000000000 --- a/projects/ontology_issue/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [oc:publication__title](http://w3id.org/ontogpt/ontology-class-templatepublication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/ontology_issue/docs/textWithTriples__publication.md b/projects/ontology_issue/docs/textWithTriples__publication.md deleted file mode 100644 index 27b0af18d..000000000 --- a/projects/ontology_issue/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [oc:textWithTriples__publication](http://w3id.org/ontogpt/ontology-class-templatetextWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ontology_issue/docs/textWithTriples__triples.md b/projects/ontology_issue/docs/textWithTriples__triples.md deleted file mode 100644 index d3a729b64..000000000 --- a/projects/ontology_issue/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [oc:textWithTriples__triples](http://w3id.org/ontogpt/ontology-class-templatetextWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/ontology_issue/docs/triple__object.md b/projects/ontology_issue/docs/triple__object.md deleted file mode 100644 index 19c663552..000000000 --- a/projects/ontology_issue/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [oc:triple__object](http://w3id.org/ontogpt/ontology-class-templatetriple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_issue/docs/triple__object_qualifier.md b/projects/ontology_issue/docs/triple__object_qualifier.md deleted file mode 100644 index bead5d4a5..000000000 --- a/projects/ontology_issue/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [oc:triple__object_qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_issue/docs/triple__predicate.md b/projects/ontology_issue/docs/triple__predicate.md deleted file mode 100644 index 425642196..000000000 --- a/projects/ontology_issue/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [oc:triple__predicate](http://w3id.org/ontogpt/ontology-class-templatetriple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_issue/docs/triple__qualifier.md b/projects/ontology_issue/docs/triple__qualifier.md deleted file mode 100644 index 9277dabfe..000000000 --- a/projects/ontology_issue/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [oc:triple__qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_issue/docs/triple__subject.md b/projects/ontology_issue/docs/triple__subject.md deleted file mode 100644 index 89487785e..000000000 --- a/projects/ontology_issue/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [oc:triple__subject](http://w3id.org/ontogpt/ontology-class-templatetriple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_issue/docs/triple__subject_qualifier.md b/projects/ontology_issue/docs/triple__subject_qualifier.md deleted file mode 100644 index e63c6bbd8..000000000 --- a/projects/ontology_issue/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [oc:triple__subject_qualifier](http://w3id.org/ontogpt/ontology-class-templatetriple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/ontology_issue/docs/types/Boolean.md b/projects/ontology_issue/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/ontology_issue/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/ontology_issue/docs/types/Curie.md b/projects/ontology_issue/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/ontology_issue/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/ontology_issue/docs/types/Date.md b/projects/ontology_issue/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/ontology_issue/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/ontology_issue/docs/types/DateOrDatetime.md b/projects/ontology_issue/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/ontology_issue/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ontology_issue/docs/types/Datetime.md b/projects/ontology_issue/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/ontology_issue/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/ontology_issue/docs/types/Decimal.md b/projects/ontology_issue/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/ontology_issue/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/ontology_issue/docs/types/Double.md b/projects/ontology_issue/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/ontology_issue/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/ontology_issue/docs/types/Float.md b/projects/ontology_issue/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/ontology_issue/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/ontology_issue/docs/types/Integer.md b/projects/ontology_issue/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/ontology_issue/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/ontology_issue/docs/types/Jsonpath.md b/projects/ontology_issue/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/ontology_issue/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ontology_issue/docs/types/Jsonpointer.md b/projects/ontology_issue/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/ontology_issue/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ontology_issue/docs/types/Ncname.md b/projects/ontology_issue/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/ontology_issue/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/ontology_issue/docs/types/Nodeidentifier.md b/projects/ontology_issue/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/ontology_issue/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/ontology_issue/docs/types/Objectidentifier.md b/projects/ontology_issue/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/ontology_issue/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/ontology_issue/docs/types/Sparqlpath.md b/projects/ontology_issue/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/ontology_issue/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/ontology_issue/docs/types/String.md b/projects/ontology_issue/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/ontology_issue/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/ontology_issue/docs/types/Time.md b/projects/ontology_issue/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/ontology_issue/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/ontology_issue/docs/types/Uri.md b/projects/ontology_issue/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/ontology_issue/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/ontology_issue/docs/types/Uriorcurie.md b/projects/ontology_issue/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/ontology_issue/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/ontology_issue/excel/ontology_issue.xlsx b/projects/ontology_issue/excel/ontology_issue.xlsx deleted file mode 100644 index 0cb00b42a376d0f150d77df12461547e19a2fda7..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 9559 zcmeHtWl)=4*KTlkD-K1AySq!V;tmChLy_VRh2k#7p-6FecXubaYq8=KzO>K0Z@+T- 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subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -interface NamedEntity - { - id: String! - label: String - } - -type OntologyChange - { - description: String - category: ChangeType - about: [OntologyClass] - } - -type OntologyClass - { - id: String! - label: String - } - -type OntologyIssue - { - title: String - summary: String - status: String - domains: [OntologyClass] - problemList: [OntologyProblem] - proposedChanges: [OntologyChange] - } - -type OntologyProblem - { - description: String - severity: String - category: ProblemType - about: [OntologyClass] - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/ontology_issue/jsonld/ontology_issue.context.jsonld b/projects/ontology_issue/jsonld/ontology_issue.context.jsonld deleted file mode 100644 index 3fd4e3438..000000000 --- a/projects/ontology_issue/jsonld/ontology_issue.context.jsonld +++ /dev/null @@ -1,151 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:55:28", - "source": "ontology_issue.yaml" - }, - "@context": { - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "oc": { - "@id": "http://w3id.org/ontogpt/ontology-class-template", - "@prefix": true - }, - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "skos": "http://www.w3.org/2004/02/skos/core#", - "@vocab": "http://w3id.org/ontogpt/ontology-class-template", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "about": { - "@type": "@id" - }, - "category": { - "@context": { - "@vocab": "@null", - "text": "skos:notation", - "description": "skos:prefLabel", - "meaning": "@id" - } - }, - "domains": { - "@type": "@id" - }, - "problem_list": { - "@type": "@id" - }, - "proposed_changes": { - "@type": "@id" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/ontology_issue/jsonld/ontology_issue.jsonld b/projects/ontology_issue/jsonld/ontology_issue.jsonld deleted file mode 100644 index 6fc9554aa..000000000 --- a/projects/ontology_issue/jsonld/ontology_issue.jsonld +++ /dev/null @@ -1,1428 +0,0 @@ -{ - "name": "ontology-issue", - "description": "A data model for representing the contents of a GitHub issue on an ontology tracker", - "title": "Ontology Issue Data Model", - "id": "https://w3id.org/ontogpt/ontology_issue", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "oc", - "prefix_reference": "http://w3id.org/ontogpt/ontology-class-template" - } - ], - "default_prefix": "oc", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "ProblemType", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateProblemType", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "permissible_values": [ - { - "text": "UNKNOWN" - }, - { - "text": "TYPO" - }, - { - "text": "BAD_XREF" - }, - { - "text": "MISSING_DEFINITION" - }, - { - "text": "MISSING_PARENT" - }, - { - "text": "BAD_RELATIONSHIP" - }, - { - "text": "OTHER" - } - ] - }, - { - "name": "ChangeType", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateChangeType", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "permissible_values": [ - { - "text": "UNKNOWN" - }, - { - "text": "CHANGE_DEFINITION" - }, - { - "text": "CHANGE_LABEL" - }, - { - "text": "CHANGE_XREF" - }, - { - "text": "MOVE_TERM" - } - ] - }, - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "ontologyIssue__title", - "description": "the title of the issue", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatetitle", - "alias": "title", - "owner": "OntologyIssue", - "domain_of": [ - "OntologyIssue" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyIssue__summary", - "annotations": [ - { - "tag": "prompt", - "value": "a high level one or two line summary of the issue, e.g. \"the definition of the class 'bone' is too vague\"", - "@type": "Annotation" - } - ], - "description": "a high level summary", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatesummary", - "alias": "summary", - "owner": "OntologyIssue", - "domain_of": [ - "OntologyIssue" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyIssue__status", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatestatus", - "alias": "status", - "owner": "OntologyIssue", - "domain_of": [ - "OntologyIssue" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyIssue__domains", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of grouping terms in the ontology.", - "@type": "Annotation" - } - ], - "description": "What part of the ontology does this pertain to.", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatedomains", - "multivalued": true, - "alias": "domains", - "owner": "OntologyIssue", - "domain_of": [ - "OntologyIssue" - ], - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "ontologyIssue__problem_list", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of problems each written as a simple statement. For example \"T cell is classified in the wrong place\"", - "@type": "Annotation" - } - ], - "description": "A list of problems stated at a high level", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templateproblem_list", - "multivalued": true, - "alias": "problem_list", - "owner": "OntologyIssue", - "domain_of": [ - "OntologyIssue" - ], - "range": "OntologyProblem", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "ontologyIssue__proposed_changes", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of grouping terms in the ontology. Example terms will be high level terms in the relevant ontology, e.g. \"skeletal system\" for an anatomy ontology.", - "@type": "Annotation" - } - ], - "description": "What part of the ontology does this pertain to.", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templateproposed_changes", - "multivalued": true, - "alias": "proposed_changes", - "owner": "OntologyIssue", - "domain_of": [ - "OntologyIssue" - ], - "range": "OntologyChange", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "ontologyProblem__description", - "description": "A succinct description of the problem", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatedescription", - "alias": "description", - "owner": "OntologyProblem", - "domain_of": [ - "OntologyProblem" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyProblem__severity", - "description": "How severe is this problem?", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templateseverity", - "alias": "severity", - "owner": "OntologyProblem", - "domain_of": [ - "OntologyProblem" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyProblem__category", - "description": "What category does this problem fall into?", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatecategory", - "alias": "category", - "owner": "OntologyProblem", - "domain_of": [ - "OntologyProblem" - ], - "range": "ProblemType", - "@type": "SlotDefinition" - }, - { - "name": "ontologyProblem__about", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of terms in the ontology that are problematic.", - "@type": "Annotation" - } - ], - "description": "What terms in the ontology is this problem about?", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templateabout", - "multivalued": true, - "alias": "about", - "owner": "OntologyProblem", - "domain_of": [ - "OntologyProblem" - ], - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "ontologyChange__description", - "description": "A succinct description of the proposed change", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatedescription", - "alias": "description", - "owner": "OntologyChange", - "domain_of": [ - "OntologyChange" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "ontologyChange__category", - "description": "What kind of change?", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templatecategory", - "alias": "category", - "owner": "OntologyChange", - "domain_of": [ - "OntologyChange" - ], - "range": "ChangeType", - "@type": "SlotDefinition" - }, - { - "name": "ontologyChange__about", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of specific terms in the ontology which will be affected by the change.", - "@type": "Annotation" - } - ], - "description": "What terms in the ontology will this change affect?", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slot_uri": "http://w3id.org/ontogpt/ontology-class-templateabout", - "multivalued": true, - "alias": "about", - "owner": "OntologyChange", - "domain_of": [ - "OntologyChange" - ], - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "OntologyIssue", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyIssue", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "slots": [ - "ontologyIssue__title", - "ontologyIssue__summary", - "ontologyIssue__status", - "ontologyIssue__domains", - "ontologyIssue__problem_list", - "ontologyIssue__proposed_changes" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "title", - "description": "the title of the issue", - "@type": "SlotDefinition" - }, - { - "name": "summary", - "annotations": [ - { - "tag": "prompt", - "value": "a high level one or two line summary of the issue, e.g. \"the definition of the class 'bone' is too vague\"", - "@type": "Annotation" - } - ], - "description": "a high level summary", - "@type": "SlotDefinition" - }, - { - "name": "status", - "@type": "SlotDefinition" - }, - { - "name": "domains", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of grouping terms in the ontology.", - "@type": "Annotation" - } - ], - "description": "What part of the ontology does this pertain to.", - "multivalued": true, - "range": "OntologyClass", - "@type": "SlotDefinition" - }, - { - "name": "problem_list", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of problems each written as a simple statement. For example \"T cell is classified in the wrong place\"", - "@type": "Annotation" - } - ], - "description": "A list of problems stated at a high level", - "multivalued": true, - "range": "OntologyProblem", - "@type": "SlotDefinition" - }, - { - "name": "proposed_changes", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of grouping terms in the ontology. Example terms will be high level terms in the relevant ontology, e.g. \"skeletal system\" for an anatomy ontology.", - "@type": "Annotation" - } - ], - "description": "What part of the ontology does this pertain to.", - "multivalued": true, - "range": "OntologyChange", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyIssue", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "OntologyClass", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyClass", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyClass", - "@type": "ClassDefinition" - }, - { - "name": "OntologyProblem", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyProblem", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "is_a": "CompoundExpression", - "slots": [ - "ontologyProblem__description", - "ontologyProblem__severity", - "ontologyProblem__category", - "ontologyProblem__about" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "description", - "description": "A succinct description of the problem", - "@type": "SlotDefinition" - }, - { - "name": "severity", - "description": "How severe is this problem?", - "@type": "SlotDefinition" - }, - { - "name": "category", - "description": "What category does this problem fall into?", - "range": "ProblemType", - "@type": "SlotDefinition" - }, - { - "name": "about", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of terms in the ontology that are problematic.", - "@type": "Annotation" - } - ], - "description": "What terms in the ontology is this problem about?", - "multivalued": true, - "range": "OntologyClass", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyProblem", - "@type": "ClassDefinition" - }, - { - "name": "OntologyChange", - "definition_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyChange", - "from_schema": "https://w3id.org/ontogpt/ontology_issue", - "is_a": "CompoundExpression", - "slots": [ - "ontologyChange__description", - "ontologyChange__category", - "ontologyChange__about" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "description", - "description": "A succinct description of the proposed change", - "@type": "SlotDefinition" - }, - { - "name": "category", - "description": "What kind of change?", - "range": "ChangeType", - "@type": "SlotDefinition" - }, - { - "name": "about", - "annotations": [ - { - "tag": "prompt", - "value": "semicolon-separated list of specific terms in the ontology which will be affected by the change.", - "@type": "Annotation" - } - ], - "description": "What terms in the ontology will this change affect?", - "multivalued": true, - "range": "OntologyClass", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/ontology-class-templateOntologyChange", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "ontology_issue.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 3383, - "generation_date": "2023-08-07T10:55:29", - "@type": "SchemaDefinition", - "@context": [ - "projects/ontology_issue/jsonld/ontology_issue.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/ontology-class-template" - } - ] -} diff --git a/projects/ontology_issue/jsonschema/ontology_issue.schema.json b/projects/ontology_issue/jsonschema/ontology_issue.schema.json deleted file mode 100644 index 211e455ba..000000000 --- a/projects/ontology_issue/jsonschema/ontology_issue.schema.json +++ /dev/null @@ -1,310 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ChangeType": { - "description": "", - "enum": [ - "UNKNOWN", - "CHANGE_DEFINITION", - "CHANGE_LABEL", - "CHANGE_XREF", - "MOVE_TERM" - ], - "title": "ChangeType", - "type": "string" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "OntologyChange": { - "additionalProperties": false, - "description": "", - "properties": { - "about": { - "description": "What terms in the ontology will this change affect?", - "items": { - "type": "string" - }, - "type": "array" - }, - "category": { - "$ref": "#/$defs/ChangeType", - "description": "What kind of change?" - }, - "description": { - "description": "A succinct description of the proposed change", - "type": "string" - } - }, - "title": "OntologyChange", - "type": "object" - }, - "OntologyClass": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "OntologyClass", - "type": "object" - }, - "OntologyIssue": { - "additionalProperties": false, - "description": "", - "properties": { - "domains": { - "description": "What part of the ontology does this pertain to.", - "items": { - "type": "string" - }, - "type": "array" - }, - "problem_list": { - "description": "A list of problems stated at a high level", - "items": { - "$ref": "#/$defs/OntologyProblem" - }, - "type": "array" - }, - "proposed_changes": { - "description": "What part of the ontology does this pertain to.", - "items": { - "$ref": "#/$defs/OntologyChange" - }, - "type": "array" - }, - "status": { - "type": "string" - }, - "summary": { - "description": "a high level summary", - "type": "string" - }, - "title": { - "description": "the title of the issue", - "type": "string" - } - }, - "title": "OntologyIssue", - "type": "object" - }, - "OntologyProblem": { - "additionalProperties": false, - "description": "", - "properties": { - "about": { - "description": "What terms in the ontology is this problem about?", - "items": { - "type": "string" - }, - "type": "array" - }, - "category": { - "$ref": "#/$defs/ProblemType", - "description": "What category does this problem fall into?" - }, - "description": { - "description": "A succinct description of the problem", - "type": "string" - }, - "severity": { - "description": "How severe is this problem?", - "type": "string" - } - }, - "title": "OntologyProblem", - "type": "object" - }, - "ProblemType": { - "description": "", - "enum": [ - "UNKNOWN", - "TYPO", - "BAD_XREF", - "MISSING_DEFINITION", - "MISSING_PARENT", - "BAD_RELATIONSHIP", - "OTHER" - ], - "title": "ProblemType", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "https://w3id.org/ontogpt/ontology_issue", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "domains": { - "description": "What part of the ontology does this pertain to.", - "items": { - "type": "string" - }, - "type": "array" - }, - "problem_list": { - "description": "A list of problems stated at a high level", - "items": { - "$ref": "#/$defs/OntologyProblem" - }, - "type": "array" - }, - "proposed_changes": { - "description": "What part of the ontology does this pertain to.", - "items": { - "$ref": "#/$defs/OntologyChange" - }, - "type": "array" - }, - "status": { - "type": "string" - }, - "summary": { - "description": "a high level summary", - "type": "string" - }, - "title": { - "description": "the title of the issue", - "type": "string" - } - }, - "title": "ontology-issue", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/ontology_issue/ontology_issue.py b/projects/ontology_issue/ontology_issue.py deleted file mode 100644 index 13815b537..000000000 --- a/projects/ontology_issue/ontology_issue.py +++ /dev/null @@ -1,550 +0,0 @@ -# Auto generated from ontology_issue.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:55:36 -# Schema: ontology-issue -# -# id: https://w3id.org/ontogpt/ontology_issue -# description: A data model for representing the contents of a GitHub issue on an ontology tracker -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -OC = CurieNamespace('oc', 'http://w3id.org/ontogpt/ontology-class-template') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = OC - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class OntologyClassId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class OntologyIssue(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.OntologyIssue - class_class_curie: ClassVar[str] = "oc:OntologyIssue" - class_name: ClassVar[str] = "OntologyIssue" - class_model_uri: ClassVar[URIRef] = OC.OntologyIssue - - title: Optional[str] = None - summary: Optional[str] = None - status: Optional[str] = None - domains: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() - problem_list: Optional[Union[Union[dict, "OntologyProblem"], List[Union[dict, "OntologyProblem"]]]] = empty_list() - proposed_changes: Optional[Union[Union[dict, "OntologyChange"], List[Union[dict, "OntologyChange"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.summary is not None and not isinstance(self.summary, str): - self.summary = str(self.summary) - - if self.status is not None and not isinstance(self.status, str): - self.status = str(self.status) - - if not isinstance(self.domains, list): - self.domains = [self.domains] if self.domains is not None else [] - self.domains = [v if isinstance(v, OntologyClassId) else OntologyClassId(v) for v in self.domains] - - if not isinstance(self.problem_list, list): - self.problem_list = [self.problem_list] if self.problem_list is not None else [] - self.problem_list = [v if isinstance(v, OntologyProblem) else OntologyProblem(**as_dict(v)) for v in self.problem_list] - - if not isinstance(self.proposed_changes, list): - self.proposed_changes = [self.proposed_changes] if self.proposed_changes is not None else [] - self.proposed_changes = [v if isinstance(v, OntologyChange) else OntologyChange(**as_dict(v)) for v in self.proposed_changes] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = OC.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = OC.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class OntologyClass(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.OntologyClass - class_class_curie: ClassVar[str] = "oc:OntologyClass" - class_name: ClassVar[str] = "OntologyClass" - class_model_uri: ClassVar[URIRef] = OC.OntologyClass - - id: Union[str, OntologyClassId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OntologyClassId): - self.id = OntologyClassId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = OC.CompoundExpression - - -@dataclass -class OntologyProblem(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.OntologyProblem - class_class_curie: ClassVar[str] = "oc:OntologyProblem" - class_name: ClassVar[str] = "OntologyProblem" - class_model_uri: ClassVar[URIRef] = OC.OntologyProblem - - description: Optional[str] = None - severity: Optional[str] = None - category: Optional[Union[str, "ProblemType"]] = None - about: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if self.severity is not None and not isinstance(self.severity, str): - self.severity = str(self.severity) - - if self.category is not None and not isinstance(self.category, ProblemType): - self.category = ProblemType(self.category) - - if not isinstance(self.about, list): - self.about = [self.about] if self.about is not None else [] - self.about = [v if isinstance(v, OntologyClassId) else OntologyClassId(v) for v in self.about] - - super().__post_init__(**kwargs) - - -@dataclass -class OntologyChange(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = OC.OntologyChange - class_class_curie: ClassVar[str] = "oc:OntologyChange" - class_name: ClassVar[str] = "OntologyChange" - class_model_uri: ClassVar[URIRef] = OC.OntologyChange - - description: Optional[str] = None - category: Optional[Union[str, "ChangeType"]] = None - about: Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if self.category is not None and not isinstance(self.category, ChangeType): - self.category = ChangeType(self.category) - - if not isinstance(self.about, list): - self.about = [self.about] if self.about is not None else [] - self.about = [v if isinstance(v, OntologyClassId) else OntologyClassId(v) for v in self.about] - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = OC.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = OC.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = OC.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = OC.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = OC.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class ProblemType(EnumDefinitionImpl): - - UNKNOWN = PermissibleValue(text="UNKNOWN") - TYPO = PermissibleValue(text="TYPO") - BAD_XREF = PermissibleValue(text="BAD_XREF") - MISSING_DEFINITION = PermissibleValue(text="MISSING_DEFINITION") - MISSING_PARENT = PermissibleValue(text="MISSING_PARENT") - BAD_RELATIONSHIP = PermissibleValue(text="BAD_RELATIONSHIP") - OTHER = PermissibleValue(text="OTHER") - - _defn = EnumDefinition( - name="ProblemType", - ) - -class ChangeType(EnumDefinitionImpl): - - UNKNOWN = PermissibleValue(text="UNKNOWN") - CHANGE_DEFINITION = PermissibleValue(text="CHANGE_DEFINITION") - CHANGE_LABEL = PermissibleValue(text="CHANGE_LABEL") - CHANGE_XREF = PermissibleValue(text="CHANGE_XREF") - MOVE_TERM = PermissibleValue(text="MOVE_TERM") - - _defn = EnumDefinition( - name="ChangeType", - ) - -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.ontologyIssue__title = Slot(uri=OC.title, name="ontologyIssue__title", curie=OC.curie('title'), - model_uri=OC.ontologyIssue__title, domain=None, range=Optional[str]) - -slots.ontologyIssue__summary = Slot(uri=OC.summary, name="ontologyIssue__summary", curie=OC.curie('summary'), - model_uri=OC.ontologyIssue__summary, domain=None, range=Optional[str]) - -slots.ontologyIssue__status = Slot(uri=OC.status, name="ontologyIssue__status", curie=OC.curie('status'), - model_uri=OC.ontologyIssue__status, domain=None, range=Optional[str]) - -slots.ontologyIssue__domains = Slot(uri=OC.domains, name="ontologyIssue__domains", curie=OC.curie('domains'), - model_uri=OC.ontologyIssue__domains, domain=None, range=Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]]) - -slots.ontologyIssue__problem_list = Slot(uri=OC.problem_list, name="ontologyIssue__problem_list", curie=OC.curie('problem_list'), - model_uri=OC.ontologyIssue__problem_list, domain=None, range=Optional[Union[Union[dict, OntologyProblem], List[Union[dict, OntologyProblem]]]]) - -slots.ontologyIssue__proposed_changes = Slot(uri=OC.proposed_changes, name="ontologyIssue__proposed_changes", curie=OC.curie('proposed_changes'), - model_uri=OC.ontologyIssue__proposed_changes, domain=None, range=Optional[Union[Union[dict, OntologyChange], List[Union[dict, OntologyChange]]]]) - -slots.ontologyProblem__description = Slot(uri=OC.description, name="ontologyProblem__description", curie=OC.curie('description'), - model_uri=OC.ontologyProblem__description, domain=None, range=Optional[str]) - -slots.ontologyProblem__severity = Slot(uri=OC.severity, name="ontologyProblem__severity", curie=OC.curie('severity'), - model_uri=OC.ontologyProblem__severity, domain=None, range=Optional[str]) - -slots.ontologyProblem__category = Slot(uri=OC.category, name="ontologyProblem__category", curie=OC.curie('category'), - model_uri=OC.ontologyProblem__category, domain=None, range=Optional[Union[str, "ProblemType"]]) - -slots.ontologyProblem__about = Slot(uri=OC.about, name="ontologyProblem__about", curie=OC.curie('about'), - model_uri=OC.ontologyProblem__about, domain=None, range=Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]]) - -slots.ontologyChange__description = Slot(uri=OC.description, name="ontologyChange__description", curie=OC.curie('description'), - model_uri=OC.ontologyChange__description, domain=None, range=Optional[str]) - -slots.ontologyChange__category = Slot(uri=OC.category, name="ontologyChange__category", curie=OC.curie('category'), - model_uri=OC.ontologyChange__category, domain=None, range=Optional[Union[str, "ChangeType"]]) - -slots.ontologyChange__about = Slot(uri=OC.about, name="ontologyChange__about", curie=OC.curie('about'), - model_uri=OC.ontologyChange__about, domain=None, range=Optional[Union[Union[str, OntologyClassId], List[Union[str, OntologyClassId]]]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=OC.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=OC.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=OC.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=OC.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=OC.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=OC.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=OC.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=OC.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=OC.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=OC.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=OC.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=OC.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=OC.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=OC.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=OC.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=OC.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=OC.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=OC.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=OC.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=OC.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=OC.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=OC.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=OC.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=OC.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=OC.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/ontology_issue/owl/ontology_issue.owl.ttl b/projects/ontology_issue/owl/ontology_issue.owl.ttl deleted file mode 100644 index a60c4b124..000000000 --- a/projects/ontology_issue/owl/ontology_issue.owl.ttl +++ /dev/null @@ -1,552 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix oc: <http://w3id.org/ontogpt/ontology-class-template> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<https://w3id.org/ontogpt/ontology_issue> a owl:Ontology ; - rdfs:label "ontology-issue" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - oc:OntologyIssue ; - linkml:classes "{'OntologyIssue': ClassDefinition(name='OntologyIssue', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateOntologyIssue', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_issue', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['ontologyIssue__title', 'ontologyIssue__summary', 'ontologyIssue__status', 'ontologyIssue__domains', 'ontologyIssue__problem_list', 'ontologyIssue__proposed_changes'], slot_usage={}, attributes={'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the title of the issue', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'summary': SlotDefinition(name='summary', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a high level one or two line summary of the issue, e.g. \"the definition of the class \\'bone\\' is too vague\"', extensions={}, annotations={})}, description='a high level summary', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'status': SlotDefinition(name='status', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'domains': SlotDefinition(name='domains', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of grouping terms in the ontology.', extensions={}, annotations={})}, description='What part of the ontology does this pertain to.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'problem_list': SlotDefinition(name='problem_list', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of problems each written as a simple statement. For example \"T cell is classified in the wrong place\"', extensions={}, annotations={})}, description='A list of problems stated at a high level', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyProblem', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'proposed_changes': SlotDefinition(name='proposed_changes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of grouping terms in the ontology. Example terms will be high level terms in the relevant ontology, e.g. \"skeletal system\" for an anatomy ontology.', extensions={}, annotations={})}, description='What part of the ontology does this pertain to.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyChange', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='oc:OntologyIssue', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'OntologyClass': ClassDefinition(name='OntologyClass', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateOntologyClass', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_issue', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='oc:OntologyClass', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'OntologyProblem': ClassDefinition(name='OntologyProblem', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateOntologyProblem', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_issue', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['ontologyProblem__description', 'ontologyProblem__severity', 'ontologyProblem__category', 'ontologyProblem__about'], slot_usage={}, attributes={'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A succinct description of the problem', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'severity': SlotDefinition(name='severity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='How severe is this problem?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'category': SlotDefinition(name='category', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='What category does this problem fall into?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ProblemType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'about': SlotDefinition(name='about', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of terms in the ontology that are problematic.', extensions={}, annotations={})}, description='What terms in the ontology is this problem about?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='oc:OntologyProblem', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'OntologyChange': ClassDefinition(name='OntologyChange', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateOntologyChange', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_issue', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['ontologyChange__description', 'ontologyChange__category', 'ontologyChange__about'], slot_usage={}, attributes={'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A succinct description of the proposed change', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'category': SlotDefinition(name='category', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='What kind of change?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChangeType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'about': SlotDefinition(name='about', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of specific terms in the ontology which will be affected by the change.', extensions={}, annotations={})}, description='What terms in the ontology will this change affect?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='oc:OntologyChange', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'ProblemType': EnumDefinition(name='ProblemType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateProblemType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_issue', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNKNOWN': PermissibleValue(text='UNKNOWN', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'TYPO': PermissibleValue(text='TYPO', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'BAD_XREF': PermissibleValue(text='BAD_XREF', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'MISSING_DEFINITION': PermissibleValue(text='MISSING_DEFINITION', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'MISSING_PARENT': PermissibleValue(text='MISSING_PARENT', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'BAD_RELATIONSHIP': PermissibleValue(text='BAD_RELATIONSHIP', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'OTHER': PermissibleValue(text='OTHER', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'ChangeType': EnumDefinition(name='ChangeType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/ontology-class-templateChangeType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/ontology_issue', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNKNOWN': PermissibleValue(text='UNKNOWN', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'CHANGE_DEFINITION': PermissibleValue(text='CHANGE_DEFINITION', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'CHANGE_LABEL': PermissibleValue(text='CHANGE_LABEL', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'CHANGE_XREF': PermissibleValue(text='CHANGE_XREF', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'MOVE_TERM': PermissibleValue(text='MOVE_TERM', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/ontology_issue" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - oc:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -oc:OntologyIssue a owl:Class, - linkml:ClassDefinition ; - rdfs:label "OntologyIssue" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:summary ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:title ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyProblem ; - owl:onProperty oc:problem_list ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:status ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyChange ; - owl:onProperty oc:proposed_changes ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyClass ; - owl:onProperty oc:domains ] ; - linkml:attributes "{'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the title of the issue', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'summary': SlotDefinition(name='summary', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a high level one or two line summary of the issue, e.g. \"the definition of the class \\'bone\\' is too vague\"', extensions={}, annotations={})}, description='a high level summary', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'status': SlotDefinition(name='status', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'domains': SlotDefinition(name='domains', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of grouping terms in the ontology.', extensions={}, annotations={})}, description='What part of the ontology does this pertain to.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'problem_list': SlotDefinition(name='problem_list', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of problems each written as a simple statement. For example \"T cell is classified in the wrong place\"', extensions={}, annotations={})}, description='A list of problems stated at a high level', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyProblem', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'proposed_changes': SlotDefinition(name='proposed_changes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of grouping terms in the ontology. Example terms will be high level terms in the relevant ontology, e.g. \"skeletal system\" for an anatomy ontology.', extensions={}, annotations={})}, description='What part of the ontology does this pertain to.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyChange', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -oc:domains a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "domains" ; - oc:prompt "semicolon-separated list of grouping terms in the ontology." ; - rdfs:range oc:OntologyClass ; - skos:definition "What part of the ontology does this pertain to." . - -oc:problem_list a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "problem_list" ; - oc:prompt "semicolon-separated list of problems each written as a simple statement. For example \"T cell is classified in the wrong place\"" ; - rdfs:range oc:OntologyProblem ; - skos:definition "A list of problems stated at a high level" . - -oc:proposed_changes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "proposed_changes" ; - oc:prompt "semicolon-separated list of grouping terms in the ontology. Example terms will be high level terms in the relevant ontology, e.g. \"skeletal system\" for an anatomy ontology." ; - rdfs:range oc:OntologyChange ; - skos:definition "What part of the ontology does this pertain to." . - -oc:severity a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "severity" ; - rdfs:range linkml:String ; - skos:definition "How severe is this problem?" . - -oc:status a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "status" ; - rdfs:range linkml:String . - -oc:summary a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "summary" ; - oc:prompt "a high level one or two line summary of the issue, e.g. \"the definition of the class 'bone' is too vague\"" ; - rdfs:range linkml:String ; - skos:definition "a high level summary" . - -oc:title a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "the title of the issue" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - oc:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_DEFINITION> a oc:ChangeType, - owl:Class ; - rdfs:label "CHANGE_DEFINITION" . - -<http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_LABEL> a oc:ChangeType, - owl:Class ; - rdfs:label "CHANGE_LABEL" . - -<http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_XREF> a oc:ChangeType, - owl:Class ; - rdfs:label "CHANGE_XREF" . - -<http://w3id.org/ontogpt/ontology-class-templateChangeType#MOVE_TERM> a oc:ChangeType, - owl:Class ; - rdfs:label "MOVE_TERM" . - -<http://w3id.org/ontogpt/ontology-class-templateChangeType#UNKNOWN> a oc:ChangeType, - owl:Class ; - rdfs:label "UNKNOWN" . - -oc:OntologyChange a owl:Class, - linkml:ClassDefinition ; - rdfs:label "OntologyChange" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:description ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyClass ; - owl:onProperty oc:about ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass oc:ChangeType ; - owl:onProperty oc:category ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A succinct description of the proposed change', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'category': SlotDefinition(name='category', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='What kind of change?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChangeType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'about': SlotDefinition(name='about', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of specific terms in the ontology which will be affected by the change.', extensions={}, annotations={})}, description='What terms in the ontology will this change affect?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -oc:OntologyProblem a owl:Class, - linkml:ClassDefinition ; - rdfs:label "OntologyProblem" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass oc:ProblemType ; - owl:onProperty oc:category ], - [ a owl:Restriction ; - owl:allValuesFrom oc:OntologyClass ; - owl:onProperty oc:about ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:severity ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty oc:description ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A succinct description of the problem', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'severity': SlotDefinition(name='severity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='How severe is this problem?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'category': SlotDefinition(name='category', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='What category does this problem fall into?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ProblemType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'about': SlotDefinition(name='about', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='semicolon-separated list of terms in the ontology that are problematic.', extensions={}, annotations={})}, description='What terms in the ontology is this problem about?', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='OntologyClass', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/ontology-class-templateProblemType#BAD_RELATIONSHIP> a oc:ProblemType, - owl:Class ; - rdfs:label "BAD_RELATIONSHIP" . - -<http://w3id.org/ontogpt/ontology-class-templateProblemType#BAD_XREF> a oc:ProblemType, - owl:Class ; - rdfs:label "BAD_XREF" . - -<http://w3id.org/ontogpt/ontology-class-templateProblemType#MISSING_DEFINITION> a oc:ProblemType, - owl:Class ; - rdfs:label "MISSING_DEFINITION" . - -<http://w3id.org/ontogpt/ontology-class-templateProblemType#MISSING_PARENT> a oc:ProblemType, - owl:Class ; - rdfs:label "MISSING_PARENT" . - -<http://w3id.org/ontogpt/ontology-class-templateProblemType#OTHER> a oc:ProblemType, - owl:Class ; - rdfs:label "OTHER" . - -<http://w3id.org/ontogpt/ontology-class-templateProblemType#TYPO> a oc:ProblemType, - owl:Class ; - rdfs:label "TYPO" . - -<http://w3id.org/ontogpt/ontology-class-templateProblemType#UNKNOWN> a oc:ProblemType, - owl:Class ; - rdfs:label "UNKNOWN" . - -oc:about a owl:ObjectProperty, - linkml:SlotDefinition . - -oc:category a owl:ObjectProperty, - linkml:SlotDefinition . - -oc:description a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -oc:OntologyClass a owl:Class, - linkml:ClassDefinition ; - rdfs:label "OntologyClass" ; - oc:annotators "sqlite:obo:go" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -oc:ChangeType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "ChangeType" ; - owl:unionOf ( <http://w3id.org/ontogpt/ontology-class-templateChangeType#UNKNOWN> <http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_DEFINITION> <http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_LABEL> <http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_XREF> <http://w3id.org/ontogpt/ontology-class-templateChangeType#MOVE_TERM> ) ; - linkml:permissible_values <http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_DEFINITION>, - <http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_LABEL>, - <http://w3id.org/ontogpt/ontology-class-templateChangeType#CHANGE_XREF>, - <http://w3id.org/ontogpt/ontology-class-templateChangeType#MOVE_TERM>, - <http://w3id.org/ontogpt/ontology-class-templateChangeType#UNKNOWN> . - -oc:ProblemType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "ProblemType" ; - owl:unionOf ( <http://w3id.org/ontogpt/ontology-class-templateProblemType#UNKNOWN> <http://w3id.org/ontogpt/ontology-class-templateProblemType#TYPO> <http://w3id.org/ontogpt/ontology-class-templateProblemType#BAD_XREF> <http://w3id.org/ontogpt/ontology-class-templateProblemType#MISSING_DEFINITION> <http://w3id.org/ontogpt/ontology-class-templateProblemType#MISSING_PARENT> <http://w3id.org/ontogpt/ontology-class-templateProblemType#BAD_RELATIONSHIP> <http://w3id.org/ontogpt/ontology-class-templateProblemType#OTHER> ) ; - linkml:permissible_values <http://w3id.org/ontogpt/ontology-class-templateProblemType#BAD_RELATIONSHIP>, - <http://w3id.org/ontogpt/ontology-class-templateProblemType#BAD_XREF>, - <http://w3id.org/ontogpt/ontology-class-templateProblemType#MISSING_DEFINITION>, - <http://w3id.org/ontogpt/ontology-class-templateProblemType#MISSING_PARENT>, - <http://w3id.org/ontogpt/ontology-class-templateProblemType#OTHER>, - <http://w3id.org/ontogpt/ontology-class-templateProblemType#TYPO>, - <http://w3id.org/ontogpt/ontology-class-templateProblemType#UNKNOWN> . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/ontology_issue/prefixmap/ontology_issue.yaml b/projects/ontology_issue/prefixmap/ontology_issue.yaml deleted file mode 100644 index d7c94693b..000000000 --- a/projects/ontology_issue/prefixmap/ontology_issue.yaml +++ /dev/null @@ -1,35 +0,0 @@ -{ - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "oc": "http://w3id.org/ontogpt/ontology-class-template", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/ontology_issue/protobuf/ontology_issue.proto b/projects/ontology_issue/protobuf/ontology_issue.proto deleted file mode 100644 index 2b363fbed..000000000 --- a/projects/ontology_issue/protobuf/ontology_issue.proto +++ /dev/null @@ -1,62 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message OntologyChange - { - string description = 0 - changeType category = 0 - repeated ontologyClass about = 0 - } -message OntologyClass - { - string id = 0 - string label = 0 - } -message OntologyIssue - { - string title = 0 - string summary = 0 - string status = 0 - repeated ontologyClass domains = 0 - repeated ontologyProblem problemList = 0 - repeated ontologyChange proposedChanges = 0 - } -message OntologyProblem - { - string description = 0 - string severity = 0 - problemType category = 0 - repeated ontologyClass about = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/ontology_issue/shacl/ontology_issue.shacl.ttl b/projects/ontology_issue/shacl/ontology_issue.shacl.ttl deleted file mode 100644 index 9b0e18cf4..000000000 --- a/projects/ontology_issue/shacl/ontology_issue.shacl.ttl +++ /dev/null @@ -1,251 +0,0 @@ -@prefix linkml: <https://w3id.org/linkml/> . -@prefix oc: <http://w3id.org/ontogpt/ontology-class-template> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -oc:OntologyIssue a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class oc:OntologyChange ; - sh:description "What part of the ontology does this pertain to." ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path oc:proposed_changes ], - [ sh:class oc:OntologyClass ; - sh:description "What part of the ontology does this pertain to." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path oc:domains ], - [ sh:class oc:OntologyProblem ; - sh:description "A list of problems stated at a high level" ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path oc:problem_list ], - [ sh:description "a high level summary" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path oc:summary ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path oc:status ], - [ sh:description "the title of the issue" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path oc:title ] ; - sh:targetClass oc:OntologyIssue . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -oc:OntologyChange a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "What kind of change?" ; - sh:in ( "UNKNOWN" "CHANGE_DEFINITION" "CHANGE_LABEL" "CHANGE_XREF" "MOVE_TERM" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path oc:category ], - [ sh:description "A succinct description of the proposed change" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path oc:description ], - [ sh:class oc:OntologyClass ; - sh:description "What terms in the ontology will this change affect?" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path oc:about ] ; - sh:targetClass oc:OntologyChange . - -oc:OntologyProblem a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A succinct description of the problem" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path oc:description ], - [ sh:description "What category does this problem fall into?" ; - sh:in ( "UNKNOWN" "TYPO" "BAD_XREF" "MISSING_DEFINITION" "MISSING_PARENT" "BAD_RELATIONSHIP" "OTHER" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path oc:category ], - [ sh:description "How severe is this problem?" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path oc:severity ], - [ sh:class oc:OntologyClass ; - sh:description "What terms in the ontology is this problem about?" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path oc:about ] ; - sh:targetClass oc:OntologyProblem . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -oc:OntologyClass a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass oc:OntologyClass . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/ontology_issue/shex/ontology_issue.shex b/projects/ontology_issue/shex/ontology_issue.shex deleted file mode 100644 index dc5c5fe35..000000000 --- a/projects/ontology_issue/shex/ontology_issue.shex +++ /dev/null @@ -1,186 +0,0 @@ -BASE <http://w3id.org/ontogpt/ontology-class-template/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - @<http://w3id.org/ontogpt/ontology-class-templateOntologyChange> OR - @<http://w3id.org/ontogpt/ontology-class-templateOntologyProblem> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -core:NamedEntity ( - @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateOntologyChange> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateOntologyChange_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <http://w3id.org/ontogpt/ontology-class-templatedescription> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatecategory> @<http://w3id.org/ontogpt/ontology-class-templateChangeType> ? - ; - <http://w3id.org/ontogpt/ontology-class-templateabout> @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> * - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateOntologyChange> ] ? - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateOntologyClass_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateOntologyClass> ] - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateOntologyIssue> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateOntologyIssue_tes> ( - <http://w3id.org/ontogpt/ontology-class-templatetitle> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatesummary> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatestatus> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatedomains> @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> - * ; - <http://w3id.org/ontogpt/ontology-class-templateproblem_list> - @<http://w3id.org/ontogpt/ontology-class-templateOntologyProblem> * ; - <http://w3id.org/ontogpt/ontology-class-templateproposed_changes> - @<http://w3id.org/ontogpt/ontology-class-templateOntologyChange> * - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateOntologyIssue> ] ? - ) -} - -<http://w3id.org/ontogpt/ontology-class-templateOntologyProblem> CLOSED { - ( $<http://w3id.org/ontogpt/ontology-class-templateOntologyProblem_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <http://w3id.org/ontogpt/ontology-class-templatedescription> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templateseverity> @linkml:String ? ; - <http://w3id.org/ontogpt/ontology-class-templatecategory> @<http://w3id.org/ontogpt/ontology-class-templateProblemType> ? - ; - <http://w3id.org/ontogpt/ontology-class-templateabout> @<http://w3id.org/ontogpt/ontology-class-templateOntologyClass> * - ) ; - rdf:type [ <http://w3id.org/ontogpt/ontology-class-templateOntologyProblem> ] ? - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/ontology_issue/sqlschema/ontology_issue.sql b/projects/ontology_issue/sqlschema/ontology_issue.sql deleted file mode 100644 index e9ae4ce38..000000000 --- a/projects/ontology_issue/sqlschema/ontology_issue.sql +++ /dev/null @@ -1,71 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "OntologyChange" ( - description TEXT, - category VARCHAR(17), - about TEXT, - PRIMARY KEY (description, category, about) -); - -CREATE TABLE "OntologyClass" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "OntologyIssue" ( - title TEXT, - summary TEXT, - status TEXT, - domains TEXT, - problem_list TEXT, - proposed_changes TEXT, - PRIMARY KEY (title, summary, status, domains, problem_list, proposed_changes) -); - -CREATE TABLE "OntologyProblem" ( - description TEXT, - severity TEXT, - category VARCHAR(18), - about TEXT, - PRIMARY KEY (description, severity, category, about) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); diff --git a/projects/phenotype/docs/AnatomicalEntity.md b/projects/phenotype/docs/AnatomicalEntity.md deleted file mode 100644 index 7fbfa471a..000000000 --- a/projects/phenotype/docs/AnatomicalEntity.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: AnatomicalEntity - - - - -URI: [phenotype:AnatomicalEntity](http://w3id.org/ontogpt/phenotype/AnatomicalEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Trait]-%20anatomical_entity%200..1>[AnatomicalEntity|id(i):string;label(i):string%20%3F],[NamedEntity]^-[AnatomicalEntity],[Trait])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Trait]-%20anatomical_entity%200..1>[AnatomicalEntity|id(i):string;label(i):string%20%3F],[NamedEntity]^-[AnatomicalEntity],[Trait]) - -## Identifier prefixes - - * UBERON - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞anatomical_entity](trait__anatomical_entity.md)* <sub>0..1</sub> **[AnatomicalEntity](AnatomicalEntity.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/phenotype/docs/AnnotatorResult.md b/projects/phenotype/docs/AnnotatorResult.md deleted file mode 100644 index 87c4ab23c..000000000 --- a/projects/phenotype/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [phenotype:AnnotatorResult](http://w3id.org/ontogpt/phenotype/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/phenotype/docs/Any.md b/projects/phenotype/docs/Any.md deleted file mode 100644 index 788bc3c44..000000000 --- a/projects/phenotype/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [phenotype:Any](http://w3id.org/ontogpt/phenotype/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/phenotype/docs/ChemicalEntity.md b/projects/phenotype/docs/ChemicalEntity.md deleted file mode 100644 index 989d382b6..000000000 --- a/projects/phenotype/docs/ChemicalEntity.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: ChemicalEntity - - - - -URI: [phenotype:ChemicalEntity](http://w3id.org/ontogpt/phenotype/ChemicalEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Trait]-%20chemical_entity%200..1>[ChemicalEntity|id(i):string;label(i):string%20%3F],[NamedEntity]^-[ChemicalEntity],[Trait])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Trait]-%20chemical_entity%200..1>[ChemicalEntity|id(i):string;label(i):string%20%3F],[NamedEntity]^-[ChemicalEntity],[Trait]) - -## Identifier prefixes - - * CHEBI - * PR - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞chemical_entity](trait__chemical_entity.md)* <sub>0..1</sub> **[ChemicalEntity](ChemicalEntity.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/phenotype/docs/CompoundExpression.md b/projects/phenotype/docs/CompoundExpression.md deleted file mode 100644 index c96367f76..000000000 --- a/projects/phenotype/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [phenotype:CompoundExpression](http://w3id.org/ontogpt/phenotype/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/phenotype/docs/ExtractionResult.md b/projects/phenotype/docs/ExtractionResult.md deleted file mode 100644 index 75c3a72ea..000000000 --- a/projects/phenotype/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [phenotype:ExtractionResult](http://w3id.org/ontogpt/phenotype/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/phenotype/docs/NamedEntity.md b/projects/phenotype/docs/NamedEntity.md deleted file mode 100644 index 037abfb20..000000000 --- a/projects/phenotype/docs/NamedEntity.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [phenotype:NamedEntity](http://w3id.org/ontogpt/phenotype/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Quality],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Quality],[NamedEntity]^-[ChemicalEntity],[NamedEntity]^-[AnatomicalEntity],[Triple],[ChemicalEntity],[AnatomicalEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[Quality],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Quality],[NamedEntity]^-[ChemicalEntity],[NamedEntity]^-[AnatomicalEntity],[Triple],[ChemicalEntity],[AnatomicalEntity]) - -## Children - - * [AnatomicalEntity](AnatomicalEntity.md) - * [ChemicalEntity](ChemicalEntity.md) - * [Quality](Quality.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/phenotype/docs/NullDataOptions.md b/projects/phenotype/docs/NullDataOptions.md deleted file mode 100644 index f0e959e56..000000000 --- a/projects/phenotype/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [phenotype:NullDataOptions](http://w3id.org/ontogpt/phenotype/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/phenotype/docs/Publication.md b/projects/phenotype/docs/Publication.md deleted file mode 100644 index e7327753c..000000000 --- a/projects/phenotype/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [phenotype:Publication](http://w3id.org/ontogpt/phenotype/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/phenotype/docs/Quality.md b/projects/phenotype/docs/Quality.md deleted file mode 100644 index b86d7fab7..000000000 --- a/projects/phenotype/docs/Quality.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Quality - - - - -URI: [phenotype:Quality](http://w3id.org/ontogpt/phenotype/Quality) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Trait]-%20quality%200..1>[Quality|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Quality],[Trait],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Trait]-%20quality%200..1>[Quality|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Quality],[Trait],[NamedEntity]) - -## Identifier prefixes - - * PATO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞quality](trait__quality.md)* <sub>0..1</sub> **[Quality](Quality.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/phenotype/docs/RelationshipType.md b/projects/phenotype/docs/RelationshipType.md deleted file mode 100644 index 928594936..000000000 --- a/projects/phenotype/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [phenotype:RelationshipType](http://w3id.org/ontogpt/phenotype/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/phenotype/docs/TextWithTriples.md b/projects/phenotype/docs/TextWithTriples.md deleted file mode 100644 index a781491ac..000000000 --- a/projects/phenotype/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [phenotype:TextWithTriples](http://w3id.org/ontogpt/phenotype/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/phenotype/docs/Trait.md b/projects/phenotype/docs/Trait.md deleted file mode 100644 index f1f31cea9..000000000 --- a/projects/phenotype/docs/Trait.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Trait - - - - -URI: [phenotype:Trait](http://w3id.org/ontogpt/phenotype/Trait) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ChemicalEntity]<chemical_entity%200..1-%20[Trait],[AnatomicalEntity]<anatomical_entity%200..1-%20[Trait],[Quality]<quality%200..1-%20[Trait],[Quality],[ChemicalEntity],[AnatomicalEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[ChemicalEntity]<chemical_entity%200..1-%20[Trait],[AnatomicalEntity]<anatomical_entity%200..1-%20[Trait],[Quality]<quality%200..1-%20[Trait],[Quality],[ChemicalEntity],[AnatomicalEntity]) - -## Attributes - - -### Own - - * [➞quality](trait__quality.md) <sub>0..1</sub> - * Description: The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration - * Range: [Quality](Quality.md) - * [➞anatomical_entity](trait__anatomical_entity.md) <sub>0..1</sub> - * Description: The anatomical location that the chemical entity is measured in - * Range: [AnatomicalEntity](AnatomicalEntity.md) - * [➞chemical_entity](trait__chemical_entity.md) <sub>0..1</sub> - * Description: The chemical entity that is being measured - * Range: [ChemicalEntity](ChemicalEntity.md) diff --git a/projects/phenotype/docs/Triple.md b/projects/phenotype/docs/Triple.md deleted file mode 100644 index a4d83f04e..000000000 --- a/projects/phenotype/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [phenotype:Triple](http://w3id.org/ontogpt/phenotype/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/phenotype/docs/annotatorResult__object_id.md b/projects/phenotype/docs/annotatorResult__object_id.md deleted file mode 100644 index 18830848d..000000000 --- a/projects/phenotype/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [phenotype:annotatorResult__object_id](http://w3id.org/ontogpt/phenotype/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/phenotype/docs/annotatorResult__object_text.md b/projects/phenotype/docs/annotatorResult__object_text.md deleted file mode 100644 index 3fa2e801b..000000000 --- a/projects/phenotype/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [phenotype:annotatorResult__object_text](http://w3id.org/ontogpt/phenotype/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/phenotype/docs/annotatorResult__subject_text.md b/projects/phenotype/docs/annotatorResult__subject_text.md deleted file mode 100644 index 0ee097512..000000000 --- a/projects/phenotype/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [phenotype:annotatorResult__subject_text](http://w3id.org/ontogpt/phenotype/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/phenotype/docs/extractionResult__extracted_object.md b/projects/phenotype/docs/extractionResult__extracted_object.md deleted file mode 100644 index 98c0ac785..000000000 --- a/projects/phenotype/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [phenotype:extractionResult__extracted_object](http://w3id.org/ontogpt/phenotype/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/phenotype/docs/extractionResult__input_id.md b/projects/phenotype/docs/extractionResult__input_id.md deleted file mode 100644 index 8c037e889..000000000 --- a/projects/phenotype/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [phenotype:extractionResult__input_id](http://w3id.org/ontogpt/phenotype/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/phenotype/docs/extractionResult__input_text.md b/projects/phenotype/docs/extractionResult__input_text.md deleted file mode 100644 index da5b1ca77..000000000 --- a/projects/phenotype/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [phenotype:extractionResult__input_text](http://w3id.org/ontogpt/phenotype/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/phenotype/docs/extractionResult__input_title.md b/projects/phenotype/docs/extractionResult__input_title.md deleted file mode 100644 index 41cca82ff..000000000 --- a/projects/phenotype/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [phenotype:extractionResult__input_title](http://w3id.org/ontogpt/phenotype/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/phenotype/docs/extractionResult__named_entities.md b/projects/phenotype/docs/extractionResult__named_entities.md deleted file mode 100644 index 31d600dbc..000000000 --- a/projects/phenotype/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [phenotype:extractionResult__named_entities](http://w3id.org/ontogpt/phenotype/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/phenotype/docs/extractionResult__prompt.md b/projects/phenotype/docs/extractionResult__prompt.md deleted file mode 100644 index d40260a23..000000000 --- a/projects/phenotype/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [phenotype:extractionResult__prompt](http://w3id.org/ontogpt/phenotype/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/phenotype/docs/extractionResult__raw_completion_output.md b/projects/phenotype/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index f6079007f..000000000 --- a/projects/phenotype/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [phenotype:extractionResult__raw_completion_output](http://w3id.org/ontogpt/phenotype/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/phenotype/docs/namedEntity__id.md b/projects/phenotype/docs/namedEntity__id.md deleted file mode 100644 index cfacc0a73..000000000 --- a/projects/phenotype/docs/namedEntity__id.md +++ /dev/null @@ -1,33 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [phenotype:namedEntity__id](http://w3id.org/ontogpt/phenotype/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnatomicalEntity](AnatomicalEntity.md) - * [ChemicalEntity](ChemicalEntity.md) - * [NamedEntity](NamedEntity.md) - * [Quality](Quality.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/phenotype/docs/namedEntity__label.md b/projects/phenotype/docs/namedEntity__label.md deleted file mode 100644 index 94431ea47..000000000 --- a/projects/phenotype/docs/namedEntity__label.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [phenotype:namedEntity__label](http://w3id.org/ontogpt/phenotype/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnatomicalEntity](AnatomicalEntity.md) - * [ChemicalEntity](ChemicalEntity.md) - * [NamedEntity](NamedEntity.md) - * [Quality](Quality.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/phenotype/docs/phenotype.md b/projects/phenotype/docs/phenotype.md deleted file mode 100644 index 92e772248..000000000 --- a/projects/phenotype/docs/phenotype.md +++ /dev/null @@ -1,110 +0,0 @@ - -# eq-template - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for Computational Phenotypes - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [AnatomicalEntity](AnatomicalEntity.md) - * [ChemicalEntity](ChemicalEntity.md) - * [Quality](Quality.md) - * [RelationshipType](RelationshipType.md) - * [Publication](Publication.md) - * [TextWithTriples](TextWithTriples.md) - * [Trait](Trait.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞anatomical_entity](trait__anatomical_entity.md) - The anatomical location that the chemical entity is measured in - * [➞chemical_entity](trait__chemical_entity.md) - The chemical entity that is being measured - * [➞quality](trait__quality.md) - The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/phenotype/docs/publication__abstract.md b/projects/phenotype/docs/publication__abstract.md deleted file mode 100644 index 3763adb02..000000000 --- a/projects/phenotype/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [phenotype:publication__abstract](http://w3id.org/ontogpt/phenotype/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/phenotype/docs/publication__combined_text.md b/projects/phenotype/docs/publication__combined_text.md deleted file mode 100644 index 755e14f97..000000000 --- a/projects/phenotype/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [phenotype:publication__combined_text](http://w3id.org/ontogpt/phenotype/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/phenotype/docs/publication__full_text.md b/projects/phenotype/docs/publication__full_text.md deleted file mode 100644 index ea9f4bbce..000000000 --- a/projects/phenotype/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [phenotype:publication__full_text](http://w3id.org/ontogpt/phenotype/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/phenotype/docs/publication__id.md b/projects/phenotype/docs/publication__id.md deleted file mode 100644 index f654e3ccc..000000000 --- a/projects/phenotype/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [phenotype:publication__id](http://w3id.org/ontogpt/phenotype/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/phenotype/docs/publication__title.md b/projects/phenotype/docs/publication__title.md deleted file mode 100644 index 1a050deba..000000000 --- a/projects/phenotype/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [phenotype:publication__title](http://w3id.org/ontogpt/phenotype/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/phenotype/docs/textWithTriples__publication.md b/projects/phenotype/docs/textWithTriples__publication.md deleted file mode 100644 index e3a2918a2..000000000 --- a/projects/phenotype/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [phenotype:textWithTriples__publication](http://w3id.org/ontogpt/phenotype/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/phenotype/docs/textWithTriples__triples.md b/projects/phenotype/docs/textWithTriples__triples.md deleted file mode 100644 index 09139f36b..000000000 --- a/projects/phenotype/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [phenotype:textWithTriples__triples](http://w3id.org/ontogpt/phenotype/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/phenotype/docs/trait__anatomical_entity.md b/projects/phenotype/docs/trait__anatomical_entity.md deleted file mode 100644 index a39a90f14..000000000 --- a/projects/phenotype/docs/trait__anatomical_entity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: anatomical_entity - - -The anatomical location that the chemical entity is measured in - -URI: [phenotype:trait__anatomical_entity](http://w3id.org/ontogpt/phenotype/trait__anatomical_entity) - - -## Domain and Range - -None → <sub>0..1</sub> [AnatomicalEntity](AnatomicalEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Trait](Trait.md) diff --git a/projects/phenotype/docs/trait__chemical_entity.md b/projects/phenotype/docs/trait__chemical_entity.md deleted file mode 100644 index b329a70aa..000000000 --- a/projects/phenotype/docs/trait__chemical_entity.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: chemical_entity - - -The chemical entity that is being measured - -URI: [phenotype:trait__chemical_entity](http://w3id.org/ontogpt/phenotype/trait__chemical_entity) - - -## Domain and Range - -None → <sub>0..1</sub> [ChemicalEntity](ChemicalEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Trait](Trait.md) diff --git a/projects/phenotype/docs/trait__quality.md b/projects/phenotype/docs/trait__quality.md deleted file mode 100644 index 55074a070..000000000 --- a/projects/phenotype/docs/trait__quality.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: quality - - -The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration - -URI: [phenotype:trait__quality](http://w3id.org/ontogpt/phenotype/trait__quality) - - -## Domain and Range - -None → <sub>0..1</sub> [Quality](Quality.md) - -## Parents - - -## Children - - -## Used by - - * [Trait](Trait.md) diff --git a/projects/phenotype/docs/triple__object.md b/projects/phenotype/docs/triple__object.md deleted file mode 100644 index 69ce54769..000000000 --- a/projects/phenotype/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [phenotype:triple__object](http://w3id.org/ontogpt/phenotype/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/phenotype/docs/triple__object_qualifier.md b/projects/phenotype/docs/triple__object_qualifier.md deleted file mode 100644 index 3ff07e51b..000000000 --- a/projects/phenotype/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [phenotype:triple__object_qualifier](http://w3id.org/ontogpt/phenotype/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/phenotype/docs/triple__predicate.md b/projects/phenotype/docs/triple__predicate.md deleted file mode 100644 index 1e69cb7d9..000000000 --- a/projects/phenotype/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [phenotype:triple__predicate](http://w3id.org/ontogpt/phenotype/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/phenotype/docs/triple__qualifier.md b/projects/phenotype/docs/triple__qualifier.md deleted file mode 100644 index 70806ec0e..000000000 --- a/projects/phenotype/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [phenotype:triple__qualifier](http://w3id.org/ontogpt/phenotype/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/phenotype/docs/triple__subject.md b/projects/phenotype/docs/triple__subject.md deleted file mode 100644 index 69cb37875..000000000 --- a/projects/phenotype/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [phenotype:triple__subject](http://w3id.org/ontogpt/phenotype/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/phenotype/docs/triple__subject_qualifier.md b/projects/phenotype/docs/triple__subject_qualifier.md deleted file mode 100644 index f59fcedfa..000000000 --- a/projects/phenotype/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [phenotype:triple__subject_qualifier](http://w3id.org/ontogpt/phenotype/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/phenotype/docs/types/Boolean.md b/projects/phenotype/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/phenotype/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/phenotype/docs/types/Curie.md b/projects/phenotype/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/phenotype/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/phenotype/docs/types/Date.md b/projects/phenotype/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/phenotype/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/phenotype/docs/types/DateOrDatetime.md b/projects/phenotype/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/phenotype/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/phenotype/docs/types/Datetime.md b/projects/phenotype/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/phenotype/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/phenotype/docs/types/Decimal.md b/projects/phenotype/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/phenotype/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/phenotype/docs/types/Double.md b/projects/phenotype/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/phenotype/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/phenotype/docs/types/Float.md b/projects/phenotype/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/phenotype/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/phenotype/docs/types/Integer.md b/projects/phenotype/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/phenotype/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/phenotype/docs/types/Jsonpath.md b/projects/phenotype/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/phenotype/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/phenotype/docs/types/Jsonpointer.md b/projects/phenotype/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/phenotype/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/phenotype/docs/types/Ncname.md b/projects/phenotype/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/phenotype/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/phenotype/docs/types/Nodeidentifier.md b/projects/phenotype/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/phenotype/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/phenotype/docs/types/Objectidentifier.md b/projects/phenotype/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/phenotype/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/phenotype/docs/types/Sparqlpath.md b/projects/phenotype/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/phenotype/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/phenotype/docs/types/String.md b/projects/phenotype/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/phenotype/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/phenotype/docs/types/Time.md b/projects/phenotype/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/phenotype/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/phenotype/docs/types/Uri.md b/projects/phenotype/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/phenotype/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/phenotype/docs/types/Uriorcurie.md b/projects/phenotype/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/phenotype/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/phenotype/excel/phenotype.xlsx b/projects/phenotype/excel/phenotype.xlsx deleted file mode 100644 index 80bd69cc1213b995cd92f61f46380262c6ad8c43..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 9180 zcmeHtbx>Pxw{CEED-K1A6)o=W7AzEpB1MY3TXC1-PH|cs+T!l+4h0GnD{eQX_ndy^ z_BZp*+&Odp`I77;dnW72yO%v{t#>QQLP28#004Nvl{%b;1gI6+4}A6ke4v95V;dtS 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String - title: String - abstract: String - combinedText: String - fullText: String - } - -type Quality - { - id: String! - label: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -type Trait - { - quality: Quality - anatomicalEntity: AnatomicalEntity - chemicalEntity: ChemicalEntity - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/phenotype/jsonld/phenotype.context.jsonld b/projects/phenotype/jsonld/phenotype.context.jsonld deleted file mode 100644 index 553f73430..000000000 --- a/projects/phenotype/jsonld/phenotype.context.jsonld +++ /dev/null @@ -1,140 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:55:41", - "source": "phenotype.yaml" - }, - "@context": { - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "PATO": "http://example.org/UNKNOWN/PATO/", - "PR": "http://example.org/UNKNOWN/PR/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "UBERON": "http://example.org/UNKNOWN/UBERON/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "phenotype": "http://w3id.org/ontogpt/phenotype/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "@vocab": "http://w3id.org/ontogpt/phenotype/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "anatomical_entity": { - "@type": "@id" - }, - "chemical_entity": { - "@type": "@id" - }, - "quality": { - "@type": "@id" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/phenotype/jsonld/phenotype.jsonld b/projects/phenotype/jsonld/phenotype.jsonld deleted file mode 100644 index eee2d6a7b..000000000 --- a/projects/phenotype/jsonld/phenotype.jsonld +++ /dev/null @@ -1,1160 +0,0 @@ -{ - "name": "eq-template", - "description": "A template for Computational Phenotypes", - "title": "EQ Template", - "id": "http://w3id.org/ontogpt/eq", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "phenotype", - "prefix_reference": "http://w3id.org/ontogpt/phenotype/" - } - ], - "default_prefix": "phenotype", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "trait__quality", - "annotations": [ - { - "tag": "prompt.example", - "value": "amount, level, increased amount, decreased concentration", - "@type": "Annotation" - } - ], - "description": "The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration", - "from_schema": "http://w3id.org/ontogpt/eq", - "slot_uri": "http://w3id.org/ontogpt/phenotype/quality", - "alias": "quality", - "owner": "Trait", - "domain_of": [ - "Trait" - ], - "range": "Quality", - "@type": "SlotDefinition" - }, - { - "name": "trait__anatomical_entity", - "annotations": [ - { - "tag": "prompt.example", - "value": "liver, heart, brain, finger", - "@type": "Annotation" - } - ], - "description": "The anatomical location that the chemical entity is measured in", - "from_schema": "http://w3id.org/ontogpt/eq", - "slot_uri": "http://w3id.org/ontogpt/phenotype/anatomical_entity", - "alias": "anatomical_entity", - "owner": "Trait", - "domain_of": [ - "Trait" - ], - "range": "AnatomicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "trait__chemical_entity", - "annotations": [ - { - "tag": "prompt.example", - "value": "lysine, metabolite", - "@type": "Annotation" - } - ], - "description": "The chemical entity that is being measured", - "from_schema": "http://w3id.org/ontogpt/eq", - "slot_uri": "http://w3id.org/ontogpt/phenotype/chemical_entity", - "alias": "chemical_entity", - "owner": "Trait", - "domain_of": [ - "Trait" - ], - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Trait", - "definition_uri": "http://w3id.org/ontogpt/phenotype/Trait", - "from_schema": "http://w3id.org/ontogpt/eq", - "slots": [ - "trait__quality", - "trait__anatomical_entity", - "trait__chemical_entity" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "quality", - "annotations": [ - { - "tag": "prompt.example", - "value": "amount, level, increased amount, decreased concentration", - "@type": "Annotation" - } - ], - "description": "The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration", - "range": "Quality", - "@type": "SlotDefinition" - }, - { - "name": "anatomical_entity", - "annotations": [ - { - "tag": "prompt.example", - "value": "liver, heart, brain, finger", - "@type": "Annotation" - } - ], - "description": "The anatomical location that the chemical entity is measured in", - "range": "AnatomicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "chemical_entity", - "annotations": [ - { - "tag": "prompt.example", - "value": "lysine, metabolite", - "@type": "Annotation" - } - ], - "description": "The chemical entity that is being measured", - "range": "ChemicalEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/phenotype/Trait", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Quality", - "id_prefixes": [ - "PATO" - ], - "definition_uri": "http://w3id.org/ontogpt/phenotype/Quality", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:pato", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/eq", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/phenotype/Quality", - "@type": "ClassDefinition" - }, - { - "name": "ChemicalEntity", - "id_prefixes": [ - "CHEBI", - "PR" - ], - "definition_uri": "http://w3id.org/ontogpt/phenotype/ChemicalEntity", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:chebi", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/eq", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/phenotype/ChemicalEntity", - "@type": "ClassDefinition" - }, - { - "name": "AnatomicalEntity", - "id_prefixes": [ - "UBERON" - ], - "definition_uri": "http://w3id.org/ontogpt/phenotype/AnatomicalEntity", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:uberon", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/eq", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/phenotype/AnatomicalEntity", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "phenotype.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 1532, - "generation_date": "2023-08-07T10:55:42", - "keywords": [ - "phenotype", - "traits" - ], - "@type": "SchemaDefinition", - "@context": [ - "projects/phenotype/jsonld/phenotype.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/phenotype/" - } - ] -} diff --git a/projects/phenotype/jsonschema/phenotype.schema.json b/projects/phenotype/jsonschema/phenotype.schema.json deleted file mode 100644 index 2917ae1bd..000000000 --- a/projects/phenotype/jsonschema/phenotype.schema.json +++ /dev/null @@ -1,232 +0,0 @@ -{ - "$defs": { - "AnatomicalEntity": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "AnatomicalEntity", - "type": "object" - }, - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ChemicalEntity": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ChemicalEntity", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "Quality": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Quality", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Trait": { - "additionalProperties": false, - "description": "", - "properties": { - "anatomical_entity": { - "description": "The anatomical location that the chemical entity is measured in", - "type": "string" - }, - "chemical_entity": { - "description": "The chemical entity that is being measured", - "type": "string" - }, - "quality": { - "description": "The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration", - "type": "string" - } - }, - "title": "Trait", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/eq", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "anatomical_entity": { - "description": "The anatomical location that the chemical entity is measured in", - "type": "string" - }, - "chemical_entity": { - "description": "The chemical entity that is being measured", - "type": "string" - }, - "quality": { - "description": "The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration", - "type": "string" - } - }, - "title": "eq-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/phenotype/owl/phenotype.owl.ttl b/projects/phenotype/owl/phenotype.owl.ttl deleted file mode 100644 index 724513002..000000000 --- a/projects/phenotype/owl/phenotype.owl.ttl +++ /dev/null @@ -1,416 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix phenotype: <http://w3id.org/ontogpt/phenotype/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/eq> a owl:Ontology ; - rdfs:label "eq-template" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - phenotype:Trait ; - linkml:classes "{'Trait': ClassDefinition(name='Trait', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/phenotype/Trait', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/eq', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['trait__quality', 'trait__anatomical_entity', 'trait__chemical_entity'], slot_usage={}, attributes={'quality': SlotDefinition(name='quality', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.example': Annotation(tag='prompt.example', value='amount, level, increased amount, decreased concentration', extensions={}, annotations={})}, description='The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Quality', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'anatomical_entity': SlotDefinition(name='anatomical_entity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.example': Annotation(tag='prompt.example', value='liver, heart, brain, finger', extensions={}, annotations={})}, description='The anatomical location that the chemical entity is measured in', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='AnatomicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'chemical_entity': SlotDefinition(name='chemical_entity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.example': Annotation(tag='prompt.example', value='lysine, metabolite', extensions={}, annotations={})}, description='The chemical entity that is being measured', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='phenotype:Trait', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Quality': ClassDefinition(name='Quality', id_prefixes=['PATO'], definition_uri='http://w3id.org/ontogpt/phenotype/Quality', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:pato', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/eq', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='phenotype:Quality', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ChemicalEntity': ClassDefinition(name='ChemicalEntity', id_prefixes=['CHEBI', 'PR'], definition_uri='http://w3id.org/ontogpt/phenotype/ChemicalEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:chebi', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/eq', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='phenotype:ChemicalEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnatomicalEntity': ClassDefinition(name='AnatomicalEntity', id_prefixes=['UBERON'], definition_uri='http://w3id.org/ontogpt/phenotype/AnatomicalEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:uberon', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/eq', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='phenotype:AnatomicalEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/eq" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - phenotype:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -phenotype:Trait a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Trait" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass phenotype:Quality ; - owl:onProperty phenotype:quality ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass phenotype:AnatomicalEntity ; - owl:onProperty phenotype:anatomical_entity ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass phenotype:ChemicalEntity ; - owl:onProperty phenotype:chemical_entity ] ; - linkml:attributes "{'quality': SlotDefinition(name='quality', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.example': Annotation(tag='prompt.example', value='amount, level, increased amount, decreased concentration', extensions={}, annotations={})}, description='The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Quality', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'anatomical_entity': SlotDefinition(name='anatomical_entity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.example': Annotation(tag='prompt.example', value='liver, heart, brain, finger', extensions={}, annotations={})}, description='The anatomical location that the chemical entity is measured in', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='AnatomicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'chemical_entity': SlotDefinition(name='chemical_entity', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.example': Annotation(tag='prompt.example', value='lysine, metabolite', extensions={}, annotations={})}, description='The chemical entity that is being measured', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -phenotype:anatomical_entity a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "anatomical_entity" ; - phenotype:prompt.example "liver, heart, brain, finger" ; - rdfs:range phenotype:AnatomicalEntity ; - skos:definition "The anatomical location that the chemical entity is measured in" . - -phenotype:chemical_entity a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "chemical_entity" ; - phenotype:prompt.example "lysine, metabolite" ; - rdfs:range phenotype:ChemicalEntity ; - skos:definition "The chemical entity that is being measured" . - -phenotype:quality a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "quality" ; - phenotype:prompt.example "amount, level, increased amount, decreased concentration" ; - rdfs:range phenotype:Quality ; - skos:definition "The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - phenotype:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -phenotype:AnatomicalEntity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnatomicalEntity" ; - phenotype:annotators "sqlite:obo:uberon" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -phenotype:ChemicalEntity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalEntity" ; - phenotype:annotators "sqlite:obo:chebi" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -phenotype:Quality a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Quality" ; - phenotype:annotators "sqlite:obo:pato" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/phenotype/phenotype.py b/projects/phenotype/phenotype.py deleted file mode 100644 index f70864d7d..000000000 --- a/projects/phenotype/phenotype.py +++ /dev/null @@ -1,473 +0,0 @@ -# Auto generated from phenotype.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:55:50 -# Schema: eq-template -# -# id: http://w3id.org/ontogpt/eq -# description: A template for Computational Phenotypes -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CHEBI = CurieNamespace('CHEBI', 'http://example.org/UNKNOWN/CHEBI/') -PATO = CurieNamespace('PATO', 'http://example.org/UNKNOWN/PATO/') -PR = CurieNamespace('PR', 'http://example.org/UNKNOWN/PR/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -UBERON = CurieNamespace('UBERON', 'http://example.org/UNKNOWN/UBERON/') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -PHENOTYPE = CurieNamespace('phenotype', 'http://w3id.org/ontogpt/phenotype/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -DEFAULT_ = PHENOTYPE - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class QualityId(NamedEntityId): - pass - - -class ChemicalEntityId(NamedEntityId): - pass - - -class AnatomicalEntityId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class Trait(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PHENOTYPE.Trait - class_class_curie: ClassVar[str] = "phenotype:Trait" - class_name: ClassVar[str] = "Trait" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.Trait - - quality: Optional[Union[str, QualityId]] = None - anatomical_entity: Optional[Union[str, AnatomicalEntityId]] = None - chemical_entity: Optional[Union[str, ChemicalEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.quality is not None and not isinstance(self.quality, QualityId): - self.quality = QualityId(self.quality) - - if self.anatomical_entity is not None and not isinstance(self.anatomical_entity, AnatomicalEntityId): - self.anatomical_entity = AnatomicalEntityId(self.anatomical_entity) - - if self.chemical_entity is not None and not isinstance(self.chemical_entity, ChemicalEntityId): - self.chemical_entity = ChemicalEntityId(self.chemical_entity) - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Quality(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PHENOTYPE.Quality - class_class_curie: ClassVar[str] = "phenotype:Quality" - class_name: ClassVar[str] = "Quality" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.Quality - - id: Union[str, QualityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, QualityId): - self.id = QualityId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalEntity(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PHENOTYPE.ChemicalEntity - class_class_curie: ClassVar[str] = "phenotype:ChemicalEntity" - class_name: ClassVar[str] = "ChemicalEntity" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.ChemicalEntity - - id: Union[str, ChemicalEntityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalEntityId): - self.id = ChemicalEntityId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class AnatomicalEntity(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = PHENOTYPE.AnatomicalEntity - class_class_curie: ClassVar[str] = "phenotype:AnatomicalEntity" - class_name: ClassVar[str] = "AnatomicalEntity" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.AnatomicalEntity - - id: Union[str, AnatomicalEntityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, AnatomicalEntityId): - self.id = AnatomicalEntityId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = PHENOTYPE.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.trait__quality = Slot(uri=PHENOTYPE.quality, name="trait__quality", curie=PHENOTYPE.curie('quality'), - model_uri=PHENOTYPE.trait__quality, domain=None, range=Optional[Union[str, QualityId]]) - -slots.trait__anatomical_entity = Slot(uri=PHENOTYPE.anatomical_entity, name="trait__anatomical_entity", curie=PHENOTYPE.curie('anatomical_entity'), - model_uri=PHENOTYPE.trait__anatomical_entity, domain=None, range=Optional[Union[str, AnatomicalEntityId]]) - -slots.trait__chemical_entity = Slot(uri=PHENOTYPE.chemical_entity, name="trait__chemical_entity", curie=PHENOTYPE.curie('chemical_entity'), - model_uri=PHENOTYPE.trait__chemical_entity, domain=None, range=Optional[Union[str, ChemicalEntityId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=PHENOTYPE.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=PHENOTYPE.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=PHENOTYPE.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=PHENOTYPE.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=PHENOTYPE.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=PHENOTYPE.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=PHENOTYPE.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=PHENOTYPE.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=PHENOTYPE.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=PHENOTYPE.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=PHENOTYPE.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=PHENOTYPE.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=PHENOTYPE.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=PHENOTYPE.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=PHENOTYPE.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=PHENOTYPE.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=PHENOTYPE.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=PHENOTYPE.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=PHENOTYPE.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=PHENOTYPE.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=PHENOTYPE.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=PHENOTYPE.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=PHENOTYPE.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=PHENOTYPE.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=PHENOTYPE.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/phenotype/prefixmap/phenotype.yaml b/projects/phenotype/prefixmap/phenotype.yaml deleted file mode 100644 index d12ea9a81..000000000 --- a/projects/phenotype/prefixmap/phenotype.yaml +++ /dev/null @@ -1,39 +0,0 @@ -{ - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "PATO": "http://example.org/UNKNOWN/PATO/", - "PR": "http://example.org/UNKNOWN/PR/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "UBERON": "http://example.org/UNKNOWN/UBERON/", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "phenotype": "http://w3id.org/ontogpt/phenotype/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/phenotype/protobuf/phenotype.proto b/projects/phenotype/protobuf/phenotype.proto deleted file mode 100644 index f8a704a2b..000000000 --- a/projects/phenotype/protobuf/phenotype.proto +++ /dev/null @@ -1,56 +0,0 @@ -message AnatomicalEntity - { - string id = 0 - string label = 0 - } -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message ChemicalEntity - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message Quality - { - string id = 0 - string label = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Trait - { - quality quality = 0 - anatomicalEntity anatomicalEntity = 0 - chemicalEntity chemicalEntity = 0 - } diff --git a/projects/phenotype/shacl/phenotype.shacl.ttl b/projects/phenotype/shacl/phenotype.shacl.ttl deleted file mode 100644 index c49528c43..000000000 --- a/projects/phenotype/shacl/phenotype.shacl.ttl +++ /dev/null @@ -1,229 +0,0 @@ -@prefix linkml: <https://w3id.org/linkml/> . -@prefix phenotype: <http://w3id.org/ontogpt/phenotype/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -phenotype:Trait a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class phenotype:Quality ; - sh:description "The property being measured, or changes in this property, for example, amount, level, increased amount, decreased concentration" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path phenotype:quality ], - [ sh:class phenotype:AnatomicalEntity ; - sh:description "The anatomical location that the chemical entity is measured in" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path phenotype:anatomical_entity ], - [ sh:class phenotype:ChemicalEntity ; - sh:description "The chemical entity that is being measured" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path phenotype:chemical_entity ] ; - sh:targetClass phenotype:Trait . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -phenotype:AnatomicalEntity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass phenotype:AnatomicalEntity . - -phenotype:ChemicalEntity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass phenotype:ChemicalEntity . - -phenotype:Quality a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass phenotype:Quality . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/phenotype/shex/phenotype.shex b/projects/phenotype/shex/phenotype.shex deleted file mode 100644 index 2c22558ee..000000000 --- a/projects/phenotype/shex/phenotype.shex +++ /dev/null @@ -1,167 +0,0 @@ -BASE <http://w3id.org/ontogpt/phenotype/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -<AnatomicalEntity> CLOSED { - ( $<AnatomicalEntity_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <AnatomicalEntity> ] - ) -} - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<ChemicalEntity> CLOSED { - ( $<ChemicalEntity_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <ChemicalEntity> ] - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -core:NamedEntity ( - @<AnatomicalEntity> OR @<ChemicalEntity> OR @<Quality> OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -<Quality> CLOSED { - ( $<Quality_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Quality> ] - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -<Trait> CLOSED { - ( $<Trait_tes> ( <quality> @<Quality> ? ; - <anatomical_entity> @<AnatomicalEntity> ? ; - <chemical_entity> @<ChemicalEntity> ? - ) ; - rdf:type [ <Trait> ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/phenotype/sqlschema/phenotype.sql b/projects/phenotype/sqlschema/phenotype.sql deleted file mode 100644 index 7bd14dd68..000000000 --- a/projects/phenotype/sqlschema/phenotype.sql +++ /dev/null @@ -1,68 +0,0 @@ - - -CREATE TABLE "AnatomicalEntity" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ChemicalEntity" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "Quality" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Trait" ( - quality TEXT, - anatomical_entity TEXT, - chemical_entity TEXT, - PRIMARY KEY (quality, anatomical_entity, chemical_entity), - FOREIGN KEY(quality) REFERENCES "Quality" (id), - FOREIGN KEY(anatomical_entity) REFERENCES "AnatomicalEntity" (id), - FOREIGN KEY(chemical_entity) REFERENCES "ChemicalEntity" (id) -); diff --git a/projects/reaction/docs/AnnotatorResult.md b/projects/reaction/docs/AnnotatorResult.md deleted file mode 100644 index 630731463..000000000 --- a/projects/reaction/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [reaction:AnnotatorResult](http://w3id.org/ontogpt/reaction/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/Any.md b/projects/reaction/docs/Any.md deleted file mode 100644 index b2f19a55a..000000000 --- a/projects/reaction/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [reaction:Any](http://w3id.org/ontogpt/reaction/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/reaction/docs/ChemicalEntity.md b/projects/reaction/docs/ChemicalEntity.md deleted file mode 100644 index c36fa7384..000000000 --- a/projects/reaction/docs/ChemicalEntity.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: ChemicalEntity - - - - -URI: [reaction:ChemicalEntity](http://w3id.org/ontogpt/reaction/ChemicalEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Reaction]-%20left_side%200..*>[ChemicalEntity|id(i):string;label(i):string%20%3F],[Reaction]-%20right_side%200..*>[ChemicalEntity],[NamedEntity]^-[ChemicalEntity],[Reaction])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Reaction]-%20left_side%200..*>[ChemicalEntity|id(i):string;label(i):string%20%3F],[Reaction]-%20right_side%200..*>[ChemicalEntity],[NamedEntity]^-[ChemicalEntity],[Reaction]) - -## Identifier prefixes - - * CHEBI - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞left_side](reaction__left_side.md)* <sub>0..\*</sub> **[ChemicalEntity](ChemicalEntity.md)** - * **None** *[➞right_side](reaction__right_side.md)* <sub>0..\*</sub> **[ChemicalEntity](ChemicalEntity.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/CompoundExpression.md b/projects/reaction/docs/CompoundExpression.md deleted file mode 100644 index 0e7601850..000000000 --- a/projects/reaction/docs/CompoundExpression.md +++ /dev/null @@ -1,21 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [reaction:CompoundExpression](http://w3id.org/ontogpt/reaction/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[GeneReactionPairing],[CompoundExpression]^-[Triple],[CompoundExpression]^-[GeneReactionPairing])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[GeneReactionPairing],[CompoundExpression]^-[Triple],[CompoundExpression]^-[GeneReactionPairing]) - -## Children - - * [GeneReactionPairing](GeneReactionPairing.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/reaction/docs/Evidence.md b/projects/reaction/docs/Evidence.md deleted file mode 100644 index 13cf7dcda..000000000 --- a/projects/reaction/docs/Evidence.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: Evidence - - - - -URI: [reaction:Evidence](http://w3id.org/ontogpt/reaction/Evidence) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[ReactionDocument]-%20has_evidence%200..*>[Evidence|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Evidence],[ReactionDocument])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[ReactionDocument]-%20has_evidence%200..*>[Evidence|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Evidence],[ReactionDocument]) - -## Identifier prefixes - - * OBI - * ECO - * MS - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞has_evidence](reactionDocument__has_evidence.md)* <sub>0..\*</sub> **[Evidence](Evidence.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/ExtractionResult.md b/projects/reaction/docs/ExtractionResult.md deleted file mode 100644 index f7dbf9d9e..000000000 --- a/projects/reaction/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [reaction:ExtractionResult](http://w3id.org/ontogpt/reaction/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/reaction/docs/Gene.md b/projects/reaction/docs/Gene.md deleted file mode 100644 index e89406d93..000000000 --- a/projects/reaction/docs/Gene.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: Gene - - - - -URI: [reaction:Gene](http://w3id.org/ontogpt/reaction/Gene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneReactionPairing]-%20gene%200..1>[Gene|id(i):string;label(i):string%20%3F],[GeneToReaction]-%20gene%200..1>[Gene],[ReactionDocument]-%20genes%200..*>[Gene],[NamedEntity]^-[Gene],[ReactionDocument],[GeneToReaction],[GeneReactionPairing])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[GeneReactionPairing]-%20gene%200..1>[Gene|id(i):string;label(i):string%20%3F],[GeneToReaction]-%20gene%200..1>[Gene],[ReactionDocument]-%20genes%200..*>[Gene],[NamedEntity]^-[Gene],[ReactionDocument],[GeneToReaction],[GeneReactionPairing]) - -## Identifier prefixes - - * HGNC - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞gene](geneReactionPairing__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞gene](geneToReaction__gene.md)* <sub>0..1</sub> **[Gene](Gene.md)** - * **None** *[➞genes](reactionDocument__genes.md)* <sub>0..\*</sub> **[Gene](Gene.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/GeneReactionPairing.md b/projects/reaction/docs/GeneReactionPairing.md deleted file mode 100644 index 8037a4490..000000000 --- a/projects/reaction/docs/GeneReactionPairing.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: GeneReactionPairing - - - - -URI: [reaction:GeneReactionPairing](http://w3id.org/ontogpt/reaction/GeneReactionPairing) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Reaction],[Reaction]<reaction%200..1-%20[GeneReactionPairing],[Gene]<gene%200..1-%20[GeneReactionPairing],[ReactionDocument]++-%20gene_reaction_pairings%200..*>[GeneReactionPairing],[CompoundExpression]^-[GeneReactionPairing],[ReactionDocument],[Gene],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Reaction],[Reaction]<reaction%200..1-%20[GeneReactionPairing],[Gene]<gene%200..1-%20[GeneReactionPairing],[ReactionDocument]++-%20gene_reaction_pairings%200..*>[GeneReactionPairing],[CompoundExpression]^-[GeneReactionPairing],[ReactionDocument],[Gene],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞gene_reaction_pairings](reactionDocument__gene_reaction_pairings.md)* <sub>0..\*</sub> **[GeneReactionPairing](GeneReactionPairing.md)** - -## Attributes - - -### Own - - * [➞gene](geneReactionPairing__gene.md) <sub>0..1</sub> - * Description: name of the gene that catalyzes the reaction - * Range: [Gene](Gene.md) - * [➞reaction](geneReactionPairing__reaction.md) <sub>0..1</sub> - * Description: equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene - * Range: [Reaction](Reaction.md) diff --git a/projects/reaction/docs/GeneToReaction.md b/projects/reaction/docs/GeneToReaction.md deleted file mode 100644 index 6da2fa107..000000000 --- a/projects/reaction/docs/GeneToReaction.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Class: GeneToReaction - - - - -URI: [reaction:GeneToReaction](http://w3id.org/ontogpt/reaction/GeneToReaction) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Reaction],[Organism],[Organism]<organism%200..1-%20[GeneToReaction],[Reaction]<reactions%200..*-++[GeneToReaction],[Gene]<gene%200..1-%20[GeneToReaction],[Gene])](https://yuml.me/diagram/nofunky;dir:TB/class/[Reaction],[Organism],[Organism]<organism%200..1-%20[GeneToReaction],[Reaction]<reactions%200..*-++[GeneToReaction],[Gene]<gene%200..1-%20[GeneToReaction],[Gene]) - -## Attributes - - -### Own - - * [➞gene](geneToReaction__gene.md) <sub>0..1</sub> - * Description: name of the gene that catalyzes the reaction - * Range: [Gene](Gene.md) - * [➞reactions](geneToReaction__reactions.md) <sub>0..\*</sub> - * Description: semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene - * Range: [Reaction](Reaction.md) - * [➞organism](geneToReaction__organism.md) <sub>0..1</sub> - * Range: [Organism](Organism.md) diff --git a/projects/reaction/docs/NamedEntity.md b/projects/reaction/docs/NamedEntity.md deleted file mode 100644 index 2d2b15016..000000000 --- a/projects/reaction/docs/NamedEntity.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [reaction:NamedEntity](http://w3id.org/ontogpt/reaction/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[ReactionGrouping],[Reaction],[Organism],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[ReactionGrouping],[NamedEntity]^-[Reaction],[NamedEntity]^-[Organism],[NamedEntity]^-[Gene],[NamedEntity]^-[Evidence],[NamedEntity]^-[ChemicalEntity],[Triple],[Gene],[Evidence],[ChemicalEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[RelationshipType],[ReactionGrouping],[Reaction],[Organism],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[ReactionGrouping],[NamedEntity]^-[Reaction],[NamedEntity]^-[Organism],[NamedEntity]^-[Gene],[NamedEntity]^-[Evidence],[NamedEntity]^-[ChemicalEntity],[Triple],[Gene],[Evidence],[ChemicalEntity]) - -## Children - - * [ChemicalEntity](ChemicalEntity.md) - * [Evidence](Evidence.md) - * [Gene](Gene.md) - * [Organism](Organism.md) - * [Reaction](Reaction.md) - * [ReactionGrouping](ReactionGrouping.md) - * [RelationshipType](RelationshipType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/NullDataOptions.md b/projects/reaction/docs/NullDataOptions.md deleted file mode 100644 index a7dc176a9..000000000 --- a/projects/reaction/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [reaction:NullDataOptions](http://w3id.org/ontogpt/reaction/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/reaction/docs/Organism.md b/projects/reaction/docs/Organism.md deleted file mode 100644 index 62b7ccf96..000000000 --- a/projects/reaction/docs/Organism.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Organism - - - - -URI: [reaction:Organism](http://w3id.org/ontogpt/reaction/Organism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneToReaction]-%20organism%200..1>[Organism|id(i):string;label(i):string%20%3F],[ReactionDocument]-%20organism%200..1>[Organism],[NamedEntity]^-[Organism],[ReactionDocument],[NamedEntity],[GeneToReaction])](https://yuml.me/diagram/nofunky;dir:TB/class/[GeneToReaction]-%20organism%200..1>[Organism|id(i):string;label(i):string%20%3F],[ReactionDocument]-%20organism%200..1>[Organism],[NamedEntity]^-[Organism],[ReactionDocument],[NamedEntity],[GeneToReaction]) - -## Identifier prefixes - - * NCBITaxon - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞organism](geneToReaction__organism.md)* <sub>0..1</sub> **[Organism](Organism.md)** - * **None** *[➞organism](reactionDocument__organism.md)* <sub>0..1</sub> **[Organism](Organism.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/Publication.md b/projects/reaction/docs/Publication.md deleted file mode 100644 index d0146decc..000000000 --- a/projects/reaction/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [reaction:Publication](http://w3id.org/ontogpt/reaction/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/ReactionDocument.md b/projects/reaction/docs/ReactionDocument.md deleted file mode 100644 index 36a8b24ca..000000000 --- a/projects/reaction/docs/ReactionDocument.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: ReactionDocument - - - - -URI: [reaction:ReactionDocument](http://w3id.org/ontogpt/reaction/ReactionDocument) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Evidence]<has_evidence%200..*-%20[ReactionDocument],[Organism]<organism%200..1-%20[ReactionDocument],[GeneReactionPairing]<gene_reaction_pairings%200..*-++[ReactionDocument],[Reaction]<reactions%200..*-++[ReactionDocument],[Gene]<genes%200..*-%20[ReactionDocument],[Reaction],[Organism],[GeneReactionPairing],[Gene],[Evidence])](https://yuml.me/diagram/nofunky;dir:TB/class/[Evidence]<has_evidence%200..*-%20[ReactionDocument],[Organism]<organism%200..1-%20[ReactionDocument],[GeneReactionPairing]<gene_reaction_pairings%200..*-++[ReactionDocument],[Reaction]<reactions%200..*-++[ReactionDocument],[Gene]<genes%200..*-%20[ReactionDocument],[Reaction],[Organism],[GeneReactionPairing],[Gene],[Evidence]) - -## Attributes - - -### Own - - * [➞genes](reactionDocument__genes.md) <sub>0..\*</sub> - * Description: semicolon separated list of genes that catalyzes the mentioned reactions - * Range: [Gene](Gene.md) - * [➞reactions](reactionDocument__reactions.md) <sub>0..\*</sub> - * Description: semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene - * Range: [Reaction](Reaction.md) - * [➞gene_reaction_pairings](reactionDocument__gene_reaction_pairings.md) <sub>0..\*</sub> - * Description: semicolon separated list of gene to reaction pairings - * Range: [GeneReactionPairing](GeneReactionPairing.md) - * [➞organism](reactionDocument__organism.md) <sub>0..1</sub> - * Range: [Organism](Organism.md) - * [➞has_evidence](reactionDocument__has_evidence.md) <sub>0..\*</sub> - * Description: evidence for the reaction - * Range: [Evidence](Evidence.md) diff --git a/projects/reaction/docs/ReactionGrouping.md b/projects/reaction/docs/ReactionGrouping.md deleted file mode 100644 index d950c2a36..000000000 --- a/projects/reaction/docs/ReactionGrouping.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: ReactionGrouping - - - - -URI: [reaction:ReactionGrouping](http://w3id.org/ontogpt/reaction/ReactionGrouping) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Reaction]-%20subclass_of%200..1>[ReactionGrouping|id(i):string;label(i):string%20%3F],[NamedEntity]^-[ReactionGrouping],[Reaction],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Reaction]-%20subclass_of%200..1>[ReactionGrouping|id(i):string;label(i):string%20%3F],[NamedEntity]^-[ReactionGrouping],[Reaction],[NamedEntity]) - -## Identifier prefixes - - * GO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞subclass_of](reaction__subclass_of.md)* <sub>0..1</sub> **[ReactionGrouping](ReactionGrouping.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/RelationshipType.md b/projects/reaction/docs/RelationshipType.md deleted file mode 100644 index 8756233da..000000000 --- a/projects/reaction/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [reaction:RelationshipType](http://w3id.org/ontogpt/reaction/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/TextWithTriples.md b/projects/reaction/docs/TextWithTriples.md deleted file mode 100644 index 36ff97b7b..000000000 --- a/projects/reaction/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [reaction:TextWithTriples](http://w3id.org/ontogpt/reaction/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/reaction/docs/Triple.md b/projects/reaction/docs/Triple.md deleted file mode 100644 index f97c07b58..000000000 --- a/projects/reaction/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [reaction:Triple](http://w3id.org/ontogpt/reaction/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/reaction/docs/annotatorResult__object_id.md b/projects/reaction/docs/annotatorResult__object_id.md deleted file mode 100644 index 3a38819b6..000000000 --- a/projects/reaction/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [reaction:annotatorResult__object_id](http://w3id.org/ontogpt/reaction/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/reaction/docs/annotatorResult__object_text.md b/projects/reaction/docs/annotatorResult__object_text.md deleted file mode 100644 index e5f9997b9..000000000 --- a/projects/reaction/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [reaction:annotatorResult__object_text](http://w3id.org/ontogpt/reaction/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/reaction/docs/annotatorResult__subject_text.md b/projects/reaction/docs/annotatorResult__subject_text.md deleted file mode 100644 index ea577a57f..000000000 --- a/projects/reaction/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [reaction:annotatorResult__subject_text](http://w3id.org/ontogpt/reaction/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/reaction/docs/extractionResult__extracted_object.md b/projects/reaction/docs/extractionResult__extracted_object.md deleted file mode 100644 index 444e2017c..000000000 --- a/projects/reaction/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [reaction:extractionResult__extracted_object](http://w3id.org/ontogpt/reaction/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/reaction/docs/extractionResult__input_id.md b/projects/reaction/docs/extractionResult__input_id.md deleted file mode 100644 index f0ecd78b8..000000000 --- a/projects/reaction/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [reaction:extractionResult__input_id](http://w3id.org/ontogpt/reaction/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/reaction/docs/extractionResult__input_text.md b/projects/reaction/docs/extractionResult__input_text.md deleted file mode 100644 index f1a85839c..000000000 --- a/projects/reaction/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [reaction:extractionResult__input_text](http://w3id.org/ontogpt/reaction/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/reaction/docs/extractionResult__input_title.md b/projects/reaction/docs/extractionResult__input_title.md deleted file mode 100644 index cba484596..000000000 --- a/projects/reaction/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [reaction:extractionResult__input_title](http://w3id.org/ontogpt/reaction/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/reaction/docs/extractionResult__named_entities.md b/projects/reaction/docs/extractionResult__named_entities.md deleted file mode 100644 index e7c2aa71d..000000000 --- a/projects/reaction/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [reaction:extractionResult__named_entities](http://w3id.org/ontogpt/reaction/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/reaction/docs/extractionResult__prompt.md b/projects/reaction/docs/extractionResult__prompt.md deleted file mode 100644 index fc74bc6c7..000000000 --- a/projects/reaction/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [reaction:extractionResult__prompt](http://w3id.org/ontogpt/reaction/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/reaction/docs/extractionResult__raw_completion_output.md b/projects/reaction/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index ceb798b8a..000000000 --- a/projects/reaction/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [reaction:extractionResult__raw_completion_output](http://w3id.org/ontogpt/reaction/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/reaction/docs/geneReactionPairing__gene.md b/projects/reaction/docs/geneReactionPairing__gene.md deleted file mode 100644 index 4a6333b14..000000000 --- a/projects/reaction/docs/geneReactionPairing__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - -name of the gene that catalyzes the reaction - -URI: [reaction:geneReactionPairing__gene](http://w3id.org/ontogpt/reaction/geneReactionPairing__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneReactionPairing](GeneReactionPairing.md) diff --git a/projects/reaction/docs/geneReactionPairing__reaction.md b/projects/reaction/docs/geneReactionPairing__reaction.md deleted file mode 100644 index 1bf183062..000000000 --- a/projects/reaction/docs/geneReactionPairing__reaction.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: reaction - - -equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene - -URI: [reaction:geneReactionPairing__reaction](http://w3id.org/ontogpt/reaction/geneReactionPairing__reaction) - - -## Domain and Range - -None → <sub>0..1</sub> [Reaction](Reaction.md) - -## Parents - - -## Children - - -## Used by - - * [GeneReactionPairing](GeneReactionPairing.md) diff --git a/projects/reaction/docs/geneToReaction__gene.md b/projects/reaction/docs/geneToReaction__gene.md deleted file mode 100644 index 9fcdfb641..000000000 --- a/projects/reaction/docs/geneToReaction__gene.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene - - -name of the gene that catalyzes the reaction - -URI: [reaction:geneToReaction__gene](http://w3id.org/ontogpt/reaction/geneToReaction__gene) - - -## Domain and Range - -None → <sub>0..1</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [GeneToReaction](GeneToReaction.md) diff --git a/projects/reaction/docs/geneToReaction__organism.md b/projects/reaction/docs/geneToReaction__organism.md deleted file mode 100644 index b2871c56e..000000000 --- a/projects/reaction/docs/geneToReaction__organism.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: organism - - - - -URI: [reaction:geneToReaction__organism](http://w3id.org/ontogpt/reaction/geneToReaction__organism) - - -## Domain and Range - -None → <sub>0..1</sub> [Organism](Organism.md) - -## Parents - - -## Children - - -## Used by - - * [GeneToReaction](GeneToReaction.md) diff --git a/projects/reaction/docs/geneToReaction__reactions.md b/projects/reaction/docs/geneToReaction__reactions.md deleted file mode 100644 index 16aaa476d..000000000 --- a/projects/reaction/docs/geneToReaction__reactions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: reactions - - -semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene - -URI: [reaction:geneToReaction__reactions](http://w3id.org/ontogpt/reaction/geneToReaction__reactions) - - -## Domain and Range - -None → <sub>0..\*</sub> [Reaction](Reaction.md) - -## Parents - - -## Children - - -## Used by - - * [GeneToReaction](GeneToReaction.md) diff --git a/projects/reaction/docs/namedEntity__id.md b/projects/reaction/docs/namedEntity__id.md deleted file mode 100644 index 30a77c19e..000000000 --- a/projects/reaction/docs/namedEntity__id.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [reaction:namedEntity__id](http://w3id.org/ontogpt/reaction/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ChemicalEntity](ChemicalEntity.md) - * [Evidence](Evidence.md) - * [Gene](Gene.md) - * [NamedEntity](NamedEntity.md) - * [Organism](Organism.md) - * [Reaction](Reaction.md) - * [ReactionGrouping](ReactionGrouping.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/reaction/docs/namedEntity__label.md b/projects/reaction/docs/namedEntity__label.md deleted file mode 100644 index 9bc9ec0da..000000000 --- a/projects/reaction/docs/namedEntity__label.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [reaction:namedEntity__label](http://w3id.org/ontogpt/reaction/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ChemicalEntity](ChemicalEntity.md) - * [Evidence](Evidence.md) - * [Gene](Gene.md) - * [NamedEntity](NamedEntity.md) - * [Organism](Organism.md) - * [ReactionGrouping](ReactionGrouping.md) - * [RelationshipType](RelationshipType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/reaction/docs/publication__abstract.md b/projects/reaction/docs/publication__abstract.md deleted file mode 100644 index cac225e17..000000000 --- a/projects/reaction/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [reaction:publication__abstract](http://w3id.org/ontogpt/reaction/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/reaction/docs/publication__combined_text.md b/projects/reaction/docs/publication__combined_text.md deleted file mode 100644 index 7f78a388a..000000000 --- a/projects/reaction/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [reaction:publication__combined_text](http://w3id.org/ontogpt/reaction/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/reaction/docs/publication__full_text.md b/projects/reaction/docs/publication__full_text.md deleted file mode 100644 index 63194f9eb..000000000 --- a/projects/reaction/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [reaction:publication__full_text](http://w3id.org/ontogpt/reaction/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/reaction/docs/publication__id.md b/projects/reaction/docs/publication__id.md deleted file mode 100644 index f146bb8b1..000000000 --- a/projects/reaction/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [reaction:publication__id](http://w3id.org/ontogpt/reaction/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/reaction/docs/publication__title.md b/projects/reaction/docs/publication__title.md deleted file mode 100644 index 693cac688..000000000 --- a/projects/reaction/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [reaction:publication__title](http://w3id.org/ontogpt/reaction/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/reaction/docs/reaction.md b/projects/reaction/docs/reaction.md deleted file mode 100644 index 38f802435..000000000 --- a/projects/reaction/docs/reaction.md +++ /dev/null @@ -1,50 +0,0 @@ - -# Class: Reaction - - - - -URI: [reaction:Reaction](http://w3id.org/ontogpt/reaction/Reaction) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ReactionGrouping],[ChemicalEntity]<right_side%200..*-%20[Reaction|label:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string],[ChemicalEntity]<left_side%200..*-%20[Reaction],[ReactionGrouping]<subclass_of%200..1-%20[Reaction],[GeneReactionPairing]-%20reaction%200..1>[Reaction],[GeneToReaction]++-%20reactions%200..*>[Reaction],[ReactionDocument]++-%20reactions%200..*>[Reaction],[NamedEntity]^-[Reaction],[ReactionDocument],[NamedEntity],[GeneToReaction],[GeneReactionPairing],[ChemicalEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[ReactionGrouping],[ChemicalEntity]<right_side%200..*-%20[Reaction|label:string%20%3F;description:string%20%3F;synonyms:string%20*;id(i):string],[ChemicalEntity]<left_side%200..*-%20[Reaction],[ReactionGrouping]<subclass_of%200..1-%20[Reaction],[GeneReactionPairing]-%20reaction%200..1>[Reaction],[GeneToReaction]++-%20reactions%200..*>[Reaction],[ReactionDocument]++-%20reactions%200..*>[Reaction],[NamedEntity]^-[Reaction],[ReactionDocument],[NamedEntity],[GeneToReaction],[GeneReactionPairing],[ChemicalEntity]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞reaction](geneReactionPairing__reaction.md)* <sub>0..1</sub> **[Reaction](Reaction.md)** - * **None** *[➞reactions](geneToReaction__reactions.md)* <sub>0..\*</sub> **[Reaction](Reaction.md)** - * **None** *[➞reactions](reactionDocument__reactions.md)* <sub>0..\*</sub> **[Reaction](Reaction.md)** - -## Attributes - - -### Own - - * [➞label](reaction__label.md) <sub>0..1</sub> - * Description: the name of the reaction - * Range: [String](types/String.md) - * [➞description](reaction__description.md) <sub>0..1</sub> - * Description: a textual description of the reaction - * Range: [String](types/String.md) - * [➞synonyms](reaction__synonyms.md) <sub>0..\*</sub> - * Description: alternative names of the reaction - * Range: [String](types/String.md) - * [➞subclass_of](reaction__subclass_of.md) <sub>0..1</sub> - * Description: the category to which this biological process belongs - * Range: [ReactionGrouping](ReactionGrouping.md) - * [➞left_side](reaction__left_side.md) <sub>0..\*</sub> - * Description: semicolon separated list of chemical entities on the left side - * Range: [ChemicalEntity](ChemicalEntity.md) - * [➞right_side](reaction__right_side.md) <sub>0..\*</sub> - * Description: semicolon separated list of chemical entities on the right side - * Range: [ChemicalEntity](ChemicalEntity.md) - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) diff --git a/projects/reaction/docs/reactionDocument__gene_reaction_pairings.md b/projects/reaction/docs/reactionDocument__gene_reaction_pairings.md deleted file mode 100644 index 82ff4ba6f..000000000 --- a/projects/reaction/docs/reactionDocument__gene_reaction_pairings.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: gene_reaction_pairings - - -semicolon separated list of gene to reaction pairings - -URI: [reaction:reactionDocument__gene_reaction_pairings](http://w3id.org/ontogpt/reaction/reactionDocument__gene_reaction_pairings) - - -## Domain and Range - -None → <sub>0..\*</sub> [GeneReactionPairing](GeneReactionPairing.md) - -## Parents - - -## Children - - -## Used by - - * [ReactionDocument](ReactionDocument.md) diff --git a/projects/reaction/docs/reactionDocument__genes.md b/projects/reaction/docs/reactionDocument__genes.md deleted file mode 100644 index 8ef05a541..000000000 --- a/projects/reaction/docs/reactionDocument__genes.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: genes - - -semicolon separated list of genes that catalyzes the mentioned reactions - -URI: [reaction:reactionDocument__genes](http://w3id.org/ontogpt/reaction/reactionDocument__genes) - - -## Domain and Range - -None → <sub>0..\*</sub> [Gene](Gene.md) - -## Parents - - -## Children - - -## Used by - - * [ReactionDocument](ReactionDocument.md) diff --git a/projects/reaction/docs/reactionDocument__has_evidence.md b/projects/reaction/docs/reactionDocument__has_evidence.md deleted file mode 100644 index 6dccc2d49..000000000 --- a/projects/reaction/docs/reactionDocument__has_evidence.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: has_evidence - - -evidence for the reaction - -URI: [reaction:reactionDocument__has_evidence](http://w3id.org/ontogpt/reaction/reactionDocument__has_evidence) - - -## Domain and Range - -None → <sub>0..\*</sub> [Evidence](Evidence.md) - -## Parents - - -## Children - - -## Used by - - * [ReactionDocument](ReactionDocument.md) diff --git a/projects/reaction/docs/reactionDocument__organism.md b/projects/reaction/docs/reactionDocument__organism.md deleted file mode 100644 index ad238ee3b..000000000 --- a/projects/reaction/docs/reactionDocument__organism.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: organism - - - - -URI: [reaction:reactionDocument__organism](http://w3id.org/ontogpt/reaction/reactionDocument__organism) - - -## Domain and Range - -None → <sub>0..1</sub> [Organism](Organism.md) - -## Parents - - -## Children - - -## Used by - - * [ReactionDocument](ReactionDocument.md) diff --git a/projects/reaction/docs/reactionDocument__reactions.md b/projects/reaction/docs/reactionDocument__reactions.md deleted file mode 100644 index a48382d74..000000000 --- a/projects/reaction/docs/reactionDocument__reactions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: reactions - - -semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene - -URI: [reaction:reactionDocument__reactions](http://w3id.org/ontogpt/reaction/reactionDocument__reactions) - - -## Domain and Range - -None → <sub>0..\*</sub> [Reaction](Reaction.md) - -## Parents - - -## Children - - -## Used by - - * [ReactionDocument](ReactionDocument.md) diff --git a/projects/reaction/docs/reaction__description.md b/projects/reaction/docs/reaction__description.md deleted file mode 100644 index 751400873..000000000 --- a/projects/reaction/docs/reaction__description.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: description - - -a textual description of the reaction - -URI: [reaction:reaction__description](http://w3id.org/ontogpt/reaction/reaction__description) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Reaction](Reaction.md) diff --git a/projects/reaction/docs/reaction__label.md b/projects/reaction/docs/reaction__label.md deleted file mode 100644 index b95206713..000000000 --- a/projects/reaction/docs/reaction__label.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: label - - -the name of the reaction - -URI: [reaction:reaction__label](http://w3id.org/ontogpt/reaction/reaction__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Reaction](Reaction.md) diff --git a/projects/reaction/docs/reaction__left_side.md b/projects/reaction/docs/reaction__left_side.md deleted file mode 100644 index cef237520..000000000 --- a/projects/reaction/docs/reaction__left_side.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: left_side - - -semicolon separated list of chemical entities on the left side - -URI: [reaction:reaction__left_side](http://w3id.org/ontogpt/reaction/reaction__left_side) - - -## Domain and Range - -None → <sub>0..\*</sub> [ChemicalEntity](ChemicalEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Reaction](Reaction.md) diff --git a/projects/reaction/docs/reaction__right_side.md b/projects/reaction/docs/reaction__right_side.md deleted file mode 100644 index 4752bd01d..000000000 --- a/projects/reaction/docs/reaction__right_side.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: right_side - - -semicolon separated list of chemical entities on the right side - -URI: [reaction:reaction__right_side](http://w3id.org/ontogpt/reaction/reaction__right_side) - - -## Domain and Range - -None → <sub>0..\*</sub> [ChemicalEntity](ChemicalEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Reaction](Reaction.md) diff --git a/projects/reaction/docs/reaction__subclass_of.md b/projects/reaction/docs/reaction__subclass_of.md deleted file mode 100644 index bf5e68de4..000000000 --- a/projects/reaction/docs/reaction__subclass_of.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subclass_of - - -the category to which this biological process belongs - -URI: [reaction:reaction__subclass_of](http://w3id.org/ontogpt/reaction/reaction__subclass_of) - - -## Domain and Range - -None → <sub>0..1</sub> [ReactionGrouping](ReactionGrouping.md) - -## Parents - - -## Children - - -## Used by - - * [Reaction](Reaction.md) diff --git a/projects/reaction/docs/reaction__synonyms.md b/projects/reaction/docs/reaction__synonyms.md deleted file mode 100644 index 96fd7bfc9..000000000 --- a/projects/reaction/docs/reaction__synonyms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: synonyms - - -alternative names of the reaction - -URI: [reaction:reaction__synonyms](http://w3id.org/ontogpt/reaction/reaction__synonyms) - - -## Domain and Range - -None → <sub>0..\*</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Reaction](Reaction.md) diff --git a/projects/reaction/docs/textWithTriples__publication.md b/projects/reaction/docs/textWithTriples__publication.md deleted file mode 100644 index 4579adbe9..000000000 --- a/projects/reaction/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [reaction:textWithTriples__publication](http://w3id.org/ontogpt/reaction/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/reaction/docs/textWithTriples__triples.md b/projects/reaction/docs/textWithTriples__triples.md deleted file mode 100644 index 37be2829b..000000000 --- a/projects/reaction/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [reaction:textWithTriples__triples](http://w3id.org/ontogpt/reaction/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/reaction/docs/triple__object.md b/projects/reaction/docs/triple__object.md deleted file mode 100644 index 8f20b1f4d..000000000 --- a/projects/reaction/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [reaction:triple__object](http://w3id.org/ontogpt/reaction/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/reaction/docs/triple__object_qualifier.md b/projects/reaction/docs/triple__object_qualifier.md deleted file mode 100644 index 1b13239cd..000000000 --- a/projects/reaction/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [reaction:triple__object_qualifier](http://w3id.org/ontogpt/reaction/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/reaction/docs/triple__predicate.md b/projects/reaction/docs/triple__predicate.md deleted file mode 100644 index 3407b24b1..000000000 --- a/projects/reaction/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [reaction:triple__predicate](http://w3id.org/ontogpt/reaction/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/reaction/docs/triple__qualifier.md b/projects/reaction/docs/triple__qualifier.md deleted file mode 100644 index dcb24101f..000000000 --- a/projects/reaction/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [reaction:triple__qualifier](http://w3id.org/ontogpt/reaction/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/reaction/docs/triple__subject.md b/projects/reaction/docs/triple__subject.md deleted file mode 100644 index 111983700..000000000 --- a/projects/reaction/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [reaction:triple__subject](http://w3id.org/ontogpt/reaction/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/reaction/docs/triple__subject_qualifier.md b/projects/reaction/docs/triple__subject_qualifier.md deleted file mode 100644 index 03bb6f816..000000000 --- a/projects/reaction/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [reaction:triple__subject_qualifier](http://w3id.org/ontogpt/reaction/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/reaction/docs/types/Boolean.md b/projects/reaction/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/reaction/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/reaction/docs/types/Curie.md b/projects/reaction/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/reaction/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/reaction/docs/types/Date.md b/projects/reaction/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/reaction/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/reaction/docs/types/DateOrDatetime.md b/projects/reaction/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/reaction/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/reaction/docs/types/Datetime.md b/projects/reaction/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/reaction/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/reaction/docs/types/Decimal.md b/projects/reaction/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/reaction/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/reaction/docs/types/Double.md b/projects/reaction/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/reaction/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/reaction/docs/types/Float.md b/projects/reaction/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/reaction/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/reaction/docs/types/Integer.md b/projects/reaction/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/reaction/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/reaction/docs/types/Jsonpath.md b/projects/reaction/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/reaction/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/reaction/docs/types/Jsonpointer.md b/projects/reaction/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/reaction/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/reaction/docs/types/Ncname.md b/projects/reaction/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/reaction/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/reaction/docs/types/Nodeidentifier.md b/projects/reaction/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/reaction/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/reaction/docs/types/Objectidentifier.md b/projects/reaction/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/reaction/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/reaction/docs/types/Sparqlpath.md b/projects/reaction/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/reaction/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/reaction/docs/types/String.md b/projects/reaction/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/reaction/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/reaction/docs/types/Time.md b/projects/reaction/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/reaction/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/reaction/docs/types/Uri.md b/projects/reaction/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/reaction/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/reaction/docs/types/Uriorcurie.md b/projects/reaction/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/reaction/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/reaction/excel/reaction.xlsx b/projects/reaction/excel/reaction.xlsx deleted file mode 100644 index 323404bd6de960be9ba07c77dda855fb4db64685..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 11637 zcmeHtWl)^mvMw5AaCb;>7zpl8@Zb^{Jm>^>2=2ihf<tg8!6mr66Wjwq5+orwXW-lW zWQUvY)V_7=*7>uCdS`|z*28+A?tc5}Uacet3x@**1%(I&`vT#GB&Z$55Axf4$b|v9 zjBSjR>}_lvo*LTPGP_z?%16orI#@8C-O7GhvQ|H&V5OMKS?zb1=H`kv7IzN3@=$G$ 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a/projects/reaction/graphql/reaction.graphql +++ /dev/null @@ -1,126 +0,0 @@ -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -type ChemicalEntity - { - id: String! - label: String - } - -interface CompoundExpression - { - } - -type Evidence - { - id: String! - label: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Gene - { - id: String! - label: String - } - -type GeneReactionPairing - { - gene: Gene - reaction: Reaction - } - -type GeneToReaction - { - gene: Gene - reactions: [Reaction] - organism: Organism - } - -interface NamedEntity - { - id: String! - label: String - } - -type Organism - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type Reaction - { - id: String! - label: String - description: String - synonyms: [String] - subclassOf: ReactionGrouping - leftSide: [ChemicalEntity] - rightSide: [ChemicalEntity] - } - -type ReactionDocument - { - genes: [Gene] - reactions: [Reaction] - geneReactionPairings: [GeneReactionPairing] - organism: Organism - hasEvidence: [Evidence] - } - -type ReactionGrouping - { - id: String! - label: String - } - -type RelationshipType - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/reaction/jsonld/reaction.context.jsonld b/projects/reaction/jsonld/reaction.context.jsonld deleted file mode 100644 index fc8c112b7..000000000 --- a/projects/reaction/jsonld/reaction.context.jsonld +++ /dev/null @@ -1,163 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:55:54", - "source": "reaction.yaml" - }, - "@context": { - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "ECO": "http://example.org/UNKNOWN/ECO/", - "GO": "http://example.org/UNKNOWN/GO/", - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "MS": "http://example.org/UNKNOWN/MS/", - "NCBITaxon": "http://example.org/UNKNOWN/NCBITaxon/", - "OBI": "http://example.org/UNKNOWN/OBI/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "reaction": { - "@type": "@id" - }, - "@vocab": "http://w3id.org/ontogpt/reaction/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "gene": { - "@type": "@id" - }, - "organism": { - "@type": "@id" - }, - "reactions": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "left_side": { - "@type": "@id" - }, - "right_side": { - "@type": "@id" - }, - "subclass_of": { - "@type": "@id" - }, - "gene_reaction_pairings": { - "@type": "@id" - }, - "genes": { - "@type": "@id" - }, - "has_evidence": { - "@type": "@id" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/reaction/jsonld/reaction.jsonld b/projects/reaction/jsonld/reaction.jsonld deleted file mode 100644 index aaad0f195..000000000 --- a/projects/reaction/jsonld/reaction.jsonld +++ /dev/null @@ -1,1474 +0,0 @@ -{ - "name": "reaction-template", - "description": "A template for reactions", - "title": "reaction Template", - "id": "https://w3id.org/ontogpt/reaction", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "reaction", - "prefix_reference": "http://w3id.org/ontogpt/reaction/" - } - ], - "default_prefix": "reaction", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "reaction__label", - "description": "the name of the reaction", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/label", - "alias": "label", - "owner": "Reaction", - "domain_of": [ - "Reaction" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "reaction__description", - "description": "a textual description of the reaction", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/description", - "alias": "description", - "owner": "Reaction", - "domain_of": [ - "Reaction" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "reaction__synonyms", - "description": "alternative names of the reaction", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/synonyms", - "multivalued": true, - "alias": "synonyms", - "owner": "Reaction", - "domain_of": [ - "Reaction" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "reaction__subclass_of", - "description": "the category to which this biological process belongs", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/subclass_of", - "alias": "subclass_of", - "owner": "Reaction", - "domain_of": [ - "Reaction" - ], - "range": "ReactionGrouping", - "@type": "SlotDefinition" - }, - { - "name": "reaction__left_side", - "description": "semicolon separated list of chemical entities on the left side", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/left_side", - "multivalued": true, - "alias": "left_side", - "owner": "Reaction", - "domain_of": [ - "Reaction" - ], - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "reaction__right_side", - "description": "semicolon separated list of chemical entities on the right side", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/right_side", - "multivalued": true, - "alias": "right_side", - "owner": "Reaction", - "domain_of": [ - "Reaction" - ], - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "geneToReaction__gene", - "description": "name of the gene that catalyzes the reaction", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/gene", - "alias": "gene", - "owner": "GeneToReaction", - "domain_of": [ - "GeneToReaction" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneToReaction__reactions", - "description": "semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/reactions", - "multivalued": true, - "alias": "reactions", - "owner": "GeneToReaction", - "domain_of": [ - "GeneToReaction" - ], - "range": "Reaction", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "geneToReaction__organism", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/organism", - "alias": "organism", - "owner": "GeneToReaction", - "domain_of": [ - "GeneToReaction" - ], - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "reactionDocument__genes", - "description": "semicolon separated list of genes that catalyzes the mentioned reactions", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/genes", - "multivalued": true, - "alias": "genes", - "owner": "ReactionDocument", - "domain_of": [ - "ReactionDocument" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "reactionDocument__reactions", - "description": "semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/reactions", - "multivalued": true, - "alias": "reactions", - "owner": "ReactionDocument", - "domain_of": [ - "ReactionDocument" - ], - "range": "Reaction", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "reactionDocument__gene_reaction_pairings", - "description": "semicolon separated list of gene to reaction pairings", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/gene_reaction_pairings", - "multivalued": true, - "alias": "gene_reaction_pairings", - "owner": "ReactionDocument", - "domain_of": [ - "ReactionDocument" - ], - "range": "GeneReactionPairing", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "reactionDocument__organism", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/organism", - "alias": "organism", - "owner": "ReactionDocument", - "domain_of": [ - "ReactionDocument" - ], - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "reactionDocument__has_evidence", - "description": "evidence for the reaction", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/has_evidence", - "multivalued": true, - "alias": "has_evidence", - "owner": "ReactionDocument", - "domain_of": [ - "ReactionDocument" - ], - "range": "Evidence", - "@type": "SlotDefinition" - }, - { - "name": "geneReactionPairing__gene", - "description": "name of the gene that catalyzes the reaction", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/gene", - "alias": "gene", - "owner": "GeneReactionPairing", - "domain_of": [ - "GeneReactionPairing" - ], - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "geneReactionPairing__reaction", - "description": "equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slot_uri": "http://w3id.org/ontogpt/reaction/reaction", - "alias": "reaction", - "owner": "GeneReactionPairing", - "domain_of": [ - "GeneReactionPairing" - ], - "range": "Reaction", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Reaction", - "definition_uri": "http://w3id.org/ontogpt/reaction/Reaction", - "from_schema": "https://w3id.org/ontogpt/reaction", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "reaction__label", - "reaction__description", - "reaction__synonyms", - "reaction__subclass_of", - "reaction__left_side", - "reaction__right_side" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "label", - "description": "the name of the reaction", - "@type": "SlotDefinition" - }, - { - "name": "description", - "description": "a textual description of the reaction", - "@type": "SlotDefinition" - }, - { - "name": "synonyms", - "description": "alternative names of the reaction", - "multivalued": true, - "@type": "SlotDefinition" - }, - { - "name": "subclass_of", - "description": "the category to which this biological process belongs", - "range": "ReactionGrouping", - "@type": "SlotDefinition" - }, - { - "name": "left_side", - "description": "semicolon separated list of chemical entities on the left side", - "multivalued": true, - "range": "ChemicalEntity", - "@type": "SlotDefinition" - }, - { - "name": "right_side", - "description": "semicolon separated list of chemical entities on the right side", - "multivalued": true, - "range": "ChemicalEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/reaction/Reaction", - "@type": "ClassDefinition" - }, - { - "name": "GeneToReaction", - "definition_uri": "http://w3id.org/ontogpt/reaction/GeneToReaction", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slots": [ - "geneToReaction__gene", - "geneToReaction__reactions", - "geneToReaction__organism" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "description": "name of the gene that catalyzes the reaction", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "reactions", - "description": "semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene", - "multivalued": true, - "range": "Reaction", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "organism", - "range": "Organism", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/reaction/GeneToReaction", - "@type": "ClassDefinition" - }, - { - "name": "ReactionDocument", - "definition_uri": "http://w3id.org/ontogpt/reaction/ReactionDocument", - "from_schema": "https://w3id.org/ontogpt/reaction", - "slots": [ - "reactionDocument__genes", - "reactionDocument__reactions", - "reactionDocument__gene_reaction_pairings", - "reactionDocument__organism", - "reactionDocument__has_evidence" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "genes", - "description": "semicolon separated list of genes that catalyzes the mentioned reactions", - "multivalued": true, - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "reactions", - "description": "semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene", - "multivalued": true, - "range": "Reaction", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "gene_reaction_pairings", - "description": "semicolon separated list of gene to reaction pairings", - "multivalued": true, - "range": "GeneReactionPairing", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "organism", - "range": "Organism", - "@type": "SlotDefinition" - }, - { - "name": "has_evidence", - "description": "evidence for the reaction", - "multivalued": true, - "range": "Evidence", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/reaction/ReactionDocument", - "@type": "ClassDefinition" - }, - { - "name": "GeneReactionPairing", - "definition_uri": "http://w3id.org/ontogpt/reaction/GeneReactionPairing", - "from_schema": "https://w3id.org/ontogpt/reaction", - "is_a": "CompoundExpression", - "slots": [ - "geneReactionPairing__gene", - "geneReactionPairing__reaction" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "gene", - "description": "name of the gene that catalyzes the reaction", - "range": "Gene", - "@type": "SlotDefinition" - }, - { - "name": "reaction", - "description": "equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene", - "range": "Reaction", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/reaction/GeneReactionPairing", - "@type": "ClassDefinition" - }, - { - "name": "ReactionGrouping", - "id_prefixes": [ - "GO" - ], - "definition_uri": "http://w3id.org/ontogpt/reaction/ReactionGrouping", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/reaction", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/reaction/ReactionGrouping", - "@type": "ClassDefinition" - }, - { - "name": "ChemicalEntity", - "id_prefixes": [ - "CHEBI" - ], - "definition_uri": "http://w3id.org/ontogpt/reaction/ChemicalEntity", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:chebi", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/reaction", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/reaction/ChemicalEntity", - "@type": "ClassDefinition" - }, - { - "name": "Evidence", - "id_prefixes": [ - "OBI", - "ECO", - "MS" - ], - "definition_uri": "http://w3id.org/ontogpt/reaction/Evidence", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:obi, sqlite:obo:eco, sqlite:obo:ms", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/reaction", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/reaction/Evidence", - "@type": "ClassDefinition" - }, - { - "name": "Gene", - "id_prefixes": [ - "HGNC" - ], - "definition_uri": "http://w3id.org/ontogpt/reaction/Gene", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, bioportal:hgnc-nr, bioportal:pr", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/reaction", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/reaction/Gene", - "@type": "ClassDefinition" - }, - { - "name": "Organism", - "id_prefixes": [ - "NCBITaxon" - ], - "definition_uri": "http://w3id.org/ontogpt/reaction/Organism", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, sqlite:obo:ncbitaxon", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/reaction", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/reaction/Organism", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "reaction.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 3187, - "generation_date": "2023-08-07T10:55:55", - "@type": "SchemaDefinition", - "@context": [ - "projects/reaction/jsonld/reaction.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/reaction/" - } - ] -} diff --git a/projects/reaction/jsonschema/reaction.schema.json b/projects/reaction/jsonschema/reaction.schema.json deleted file mode 100644 index 412202eba..000000000 --- a/projects/reaction/jsonschema/reaction.schema.json +++ /dev/null @@ -1,407 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ChemicalEntity": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ChemicalEntity", - "type": "object" - }, - "Evidence": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Evidence", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Gene": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Gene", - "type": "object" - }, - "GeneReactionPairing": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "description": "name of the gene that catalyzes the reaction", - "type": "string" - }, - "reaction": { - "description": "equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene", - "type": "string" - } - }, - "title": "GeneReactionPairing", - "type": "object" - }, - "GeneToReaction": { - "additionalProperties": false, - "description": "", - "properties": { - "gene": { - "description": "name of the gene that catalyzes the reaction", - "type": "string" - }, - "organism": { - "type": "string" - }, - "reactions": { - "additionalProperties": { - "$ref": "#/$defs/Reaction__identifier_optional" - }, - "description": "semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene", - "type": "object" - } - }, - "title": "GeneToReaction", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Organism": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Organism", - "type": "object" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "Reaction": { - "additionalProperties": false, - "description": "", - "properties": { - "description": { - "description": "a textual description of the reaction", - "type": "string" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "the name of the reaction", - "type": "string" - }, - "left_side": { - "description": "semicolon separated list of chemical entities on the left side", - "items": { - "type": "string" - }, - "type": "array" - }, - "right_side": { - "description": "semicolon separated list of chemical entities on the right side", - "items": { - "type": "string" - }, - "type": "array" - }, - "subclass_of": { - "description": "the category to which this biological process belongs", - "type": "string" - }, - "synonyms": { - "description": "alternative names of the reaction", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [ - "id" - ], - "title": "Reaction", - "type": "object" - }, - "ReactionDocument": { - "additionalProperties": false, - "description": "", - "properties": { - "gene_reaction_pairings": { - "description": "semicolon separated list of gene to reaction pairings", - "items": { - "$ref": "#/$defs/GeneReactionPairing" - }, - "type": "array" - }, - "genes": { - "description": "semicolon separated list of genes that catalyzes the mentioned reactions", - "items": { - "type": "string" - }, - "type": "array" - }, - "has_evidence": { - "description": "evidence for the reaction", - "items": { - "type": "string" - }, - "type": "array" - }, - "organism": { - "type": "string" - }, - "reactions": { - "additionalProperties": { - "$ref": "#/$defs/Reaction__identifier_optional" - }, - "description": "semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene", - "type": "object" - } - }, - "title": "ReactionDocument", - "type": "object" - }, - "ReactionGrouping": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "ReactionGrouping", - "type": "object" - }, - "Reaction__identifier_optional": { - "additionalProperties": false, - "description": "", - "properties": { - "description": { - "description": "a textual description of the reaction", - "type": "string" - }, - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "the name of the reaction", - "type": "string" - }, - "left_side": { - "description": "semicolon separated list of chemical entities on the left side", - "items": { - "type": "string" - }, - "type": "array" - }, - "right_side": { - "description": "semicolon separated list of chemical entities on the right side", - "items": { - "type": "string" - }, - "type": "array" - }, - "subclass_of": { - "description": "the category to which this biological process belongs", - "type": "string" - }, - "synonyms": { - "description": "alternative names of the reaction", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "required": [], - "title": "Reaction", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - } - }, - "$id": "https://w3id.org/ontogpt/reaction", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "title": "reaction-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/reaction/owl/reaction.owl.ttl b/projects/reaction/owl/reaction.owl.ttl deleted file mode 100644 index c50abc2c2..000000000 --- a/projects/reaction/owl/reaction.owl.ttl +++ /dev/null @@ -1,544 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix reaction: <http://w3id.org/ontogpt/reaction/> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<https://w3id.org/ontogpt/reaction> a owl:Ontology ; - rdfs:label "reaction-template" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - reaction:GeneToReaction, - reaction:ReactionDocument ; - linkml:classes "{'Reaction': ClassDefinition(name='Reaction', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/reaction/Reaction', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'reaction__label', 'reaction__description', 'reaction__synonyms', 'reaction__subclass_of', 'reaction__left_side', 'reaction__right_side'], slot_usage={}, attributes={'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='alternative names of the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the category to which this biological process belongs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ReactionGrouping', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'left_side': SlotDefinition(name='left_side', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of chemical entities on the left side', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'right_side': SlotDefinition(name='right_side', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of chemical entities on the right side', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='reaction:Reaction', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneToReaction': ClassDefinition(name='GeneToReaction', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/reaction/GeneToReaction', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneToReaction__gene', 'geneToReaction__reactions', 'geneToReaction__organism'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='name of the gene that catalyzes the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'reactions': SlotDefinition(name='reactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Reaction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organism': SlotDefinition(name='organism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='reaction:GeneToReaction', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ReactionDocument': ClassDefinition(name='ReactionDocument', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/reaction/ReactionDocument', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['reactionDocument__genes', 'reactionDocument__reactions', 'reactionDocument__gene_reaction_pairings', 'reactionDocument__organism', 'reactionDocument__has_evidence'], slot_usage={}, attributes={'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of genes that catalyzes the mentioned reactions', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'reactions': SlotDefinition(name='reactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Reaction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_reaction_pairings': SlotDefinition(name='gene_reaction_pairings', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of gene to reaction pairings', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneReactionPairing', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organism': SlotDefinition(name='organism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'has_evidence': SlotDefinition(name='has_evidence', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='evidence for the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Evidence', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='reaction:ReactionDocument', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'GeneReactionPairing': ClassDefinition(name='GeneReactionPairing', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/reaction/GeneReactionPairing', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['geneReactionPairing__gene', 'geneReactionPairing__reaction'], slot_usage={}, attributes={'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='name of the gene that catalyzes the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'reaction': SlotDefinition(name='reaction', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Reaction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='reaction:GeneReactionPairing', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ReactionGrouping': ClassDefinition(name='ReactionGrouping', id_prefixes=['GO'], definition_uri='http://w3id.org/ontogpt/reaction/ReactionGrouping', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='reaction:ReactionGrouping', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ChemicalEntity': ClassDefinition(name='ChemicalEntity', id_prefixes=['CHEBI'], definition_uri='http://w3id.org/ontogpt/reaction/ChemicalEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:chebi', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='reaction:ChemicalEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Evidence': ClassDefinition(name='Evidence', id_prefixes=['OBI', 'ECO', 'MS'], definition_uri='http://w3id.org/ontogpt/reaction/Evidence', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:obi, sqlite:obo:eco, sqlite:obo:ms', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='reaction:Evidence', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC'], definition_uri='http://w3id.org/ontogpt/reaction/Gene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, bioportal:hgnc-nr, bioportal:pr', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='reaction:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Organism': ClassDefinition(name='Organism', id_prefixes=['NCBITaxon'], definition_uri='http://w3id.org/ontogpt/reaction/Organism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, sqlite:obo:ncbitaxon', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/reaction', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='reaction:Organism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/reaction" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - reaction:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -reaction:GeneToReaction a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneToReaction" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass reaction:Gene ; - owl:onProperty reaction:gene ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass reaction:Organism ; - owl:onProperty reaction:organism ], - [ a owl:Restriction ; - owl:allValuesFrom reaction:Reaction ; - owl:onProperty reaction:reactions ] ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='name of the gene that catalyzes the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'reactions': SlotDefinition(name='reactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Reaction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organism': SlotDefinition(name='organism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -reaction:ReactionDocument a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ReactionDocument" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom reaction:GeneReactionPairing ; - owl:onProperty reaction:gene_reaction_pairings ], - [ a owl:Restriction ; - owl:allValuesFrom reaction:Gene ; - owl:onProperty reaction:genes ], - [ a owl:Restriction ; - owl:allValuesFrom reaction:Reaction ; - owl:onProperty reaction:reactions ], - [ a owl:Restriction ; - owl:allValuesFrom reaction:Evidence ; - owl:onProperty reaction:has_evidence ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass reaction:Organism ; - owl:onProperty reaction:organism ] ; - linkml:attributes "{'genes': SlotDefinition(name='genes', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of genes that catalyzes the mentioned reactions', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'reactions': SlotDefinition(name='reactions', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Reaction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'gene_reaction_pairings': SlotDefinition(name='gene_reaction_pairings', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of gene to reaction pairings', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='GeneReactionPairing', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'organism': SlotDefinition(name='organism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Organism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'has_evidence': SlotDefinition(name='has_evidence', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='evidence for the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Evidence', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -reaction:description a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "description" ; - rdfs:range linkml:String ; - skos:definition "a textual description of the reaction" . - -reaction:gene_reaction_pairings a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "gene_reaction_pairings" ; - rdfs:range reaction:GeneReactionPairing ; - skos:definition "semicolon separated list of gene to reaction pairings" . - -reaction:genes a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "genes" ; - rdfs:range reaction:Gene ; - skos:definition "semicolon separated list of genes that catalyzes the mentioned reactions" . - -reaction:has_evidence a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "has_evidence" ; - rdfs:range reaction:Evidence ; - skos:definition "evidence for the reaction" . - -reaction:label a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - rdfs:range linkml:String ; - skos:definition "the name of the reaction" . - -reaction:left_side a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "left_side" ; - rdfs:range reaction:ChemicalEntity ; - skos:definition "semicolon separated list of chemical entities on the left side" . - -reaction:reaction a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "reaction" ; - rdfs:range reaction:Reaction ; - skos:definition "equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene" . - -reaction:right_side a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "right_side" ; - rdfs:range reaction:ChemicalEntity ; - skos:definition "semicolon separated list of chemical entities on the right side" . - -reaction:subclass_of a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subclass_of" ; - rdfs:range reaction:ReactionGrouping ; - skos:definition "the category to which this biological process belongs" . - -reaction:synonyms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "synonyms" ; - rdfs:range linkml:String ; - skos:definition "alternative names of the reaction" . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - reaction:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -reaction:Evidence a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Evidence" ; - reaction:annotators "sqlite:obo:obi, sqlite:obo:eco, sqlite:obo:ms" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -reaction:GeneReactionPairing a owl:Class, - linkml:ClassDefinition ; - rdfs:label "GeneReactionPairing" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass reaction:Reaction ; - owl:onProperty reaction:reaction ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass reaction:Gene ; - owl:onProperty reaction:gene ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'gene': SlotDefinition(name='gene', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='name of the gene that catalyzes the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Gene', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'reaction': SlotDefinition(name='reaction', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Reaction', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -reaction:Organism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Organism" ; - reaction:annotators "gilda:, sqlite:obo:ncbitaxon" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -reaction:ReactionGrouping a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ReactionGrouping" ; - reaction:annotators "sqlite:obo:go" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -reaction:gene a owl:ObjectProperty, - linkml:SlotDefinition . - -reaction:organism a owl:ObjectProperty, - linkml:SlotDefinition . - -reaction:reactions a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -reaction:ChemicalEntity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ChemicalEntity" ; - reaction:annotators "sqlite:obo:chebi" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -reaction:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - reaction:annotators "gilda:, bioportal:hgnc-nr, bioportal:pr" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -reaction:Reaction a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Reaction" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom reaction:ChemicalEntity ; - owl:onProperty reaction:left_side ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty reaction:description ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass reaction:ReactionGrouping ; - owl:onProperty reaction:subclass_of ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty reaction:label ], - [ a owl:Restriction ; - owl:allValuesFrom reaction:ChemicalEntity ; - owl:onProperty reaction:right_side ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty reaction:synonyms ], - <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a textual description of the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'synonyms': SlotDefinition(name='synonyms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='alternative names of the reaction', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subclass_of': SlotDefinition(name='subclass_of', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the category to which this biological process belongs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ReactionGrouping', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'left_side': SlotDefinition(name='left_side', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of chemical entities on the left side', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'right_side': SlotDefinition(name='right_side', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon separated list of chemical entities on the right side', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='ChemicalEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/reaction/prefixmap/reaction.yaml b/projects/reaction/prefixmap/reaction.yaml deleted file mode 100644 index c55f40b7c..000000000 --- a/projects/reaction/prefixmap/reaction.yaml +++ /dev/null @@ -1,42 +0,0 @@ -{ - "CHEBI": "http://example.org/UNKNOWN/CHEBI/", - "ECO": "http://example.org/UNKNOWN/ECO/", - "GO": "http://example.org/UNKNOWN/GO/", - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "MS": "http://example.org/UNKNOWN/MS/", - "NCBITaxon": "http://example.org/UNKNOWN/NCBITaxon/", - "OBI": "http://example.org/UNKNOWN/OBI/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "reaction": "http://w3id.org/ontogpt/reaction/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/reaction/protobuf/reaction.proto b/projects/reaction/protobuf/reaction.proto deleted file mode 100644 index 4b4294df0..000000000 --- a/projects/reaction/protobuf/reaction.proto +++ /dev/null @@ -1,89 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message ChemicalEntity - { - string id = 0 - string label = 0 - } -message Evidence - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -message GeneReactionPairing - { - gene gene = 0 - reaction reaction = 0 - } -message GeneToReaction - { - gene gene = 0 - repeated reaction reactions = 0 - organism organism = 0 - } -message Organism - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message Reaction - { - string id = 0 - string label = 0 - string description = 0 - repeated string synonyms = 0 - reactionGrouping subclassOf = 0 - repeated chemicalEntity leftSide = 0 - repeated chemicalEntity rightSide = 0 - } -message ReactionDocument - { - repeated gene genes = 0 - repeated reaction reactions = 0 - repeated geneReactionPairing geneReactionPairings = 0 - organism organism = 0 - repeated evidence hasEvidence = 0 - } -message ReactionGrouping - { - string id = 0 - string label = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } diff --git a/projects/reaction/reaction.py b/projects/reaction/reaction.py deleted file mode 100644 index a1b30abf3..000000000 --- a/projects/reaction/reaction.py +++ /dev/null @@ -1,671 +0,0 @@ -# Auto generated from reaction.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:56:03 -# Schema: reaction-template -# -# id: https://w3id.org/ontogpt/reaction -# description: A template for reactions -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -CHEBI = CurieNamespace('CHEBI', 'http://example.org/UNKNOWN/CHEBI/') -ECO = CurieNamespace('ECO', 'http://example.org/UNKNOWN/ECO/') -GO = CurieNamespace('GO', 'http://example.org/UNKNOWN/GO/') -HGNC = CurieNamespace('HGNC', 'http://example.org/UNKNOWN/HGNC/') -MS = CurieNamespace('MS', 'http://example.org/UNKNOWN/MS/') -NCBITAXON = CurieNamespace('NCBITaxon', 'http://example.org/UNKNOWN/NCBITaxon/') -OBI = CurieNamespace('OBI', 'http://example.org/UNKNOWN/OBI/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -REACTION = CurieNamespace('reaction', 'http://w3id.org/ontogpt/reaction/') -DEFAULT_ = REACTION - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class ReactionId(NamedEntityId): - pass - - -class ReactionGroupingId(NamedEntityId): - pass - - -class ChemicalEntityId(NamedEntityId): - pass - - -class EvidenceId(NamedEntityId): - pass - - -class GeneId(NamedEntityId): - pass - - -class OrganismId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class GeneToReaction(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.GeneToReaction - class_class_curie: ClassVar[str] = "reaction:GeneToReaction" - class_name: ClassVar[str] = "GeneToReaction" - class_model_uri: ClassVar[URIRef] = REACTION.GeneToReaction - - gene: Optional[Union[str, GeneId]] = None - reactions: Optional[Union[Dict[Union[str, ReactionId], Union[dict, Reaction]], List[Union[dict, Reaction]]]] = empty_dict() - organism: Optional[Union[str, OrganismId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - self._normalize_inlined_as_dict(slot_name="reactions", slot_type=Reaction, key_name="id", keyed=True) - - if self.organism is not None and not isinstance(self.organism, OrganismId): - self.organism = OrganismId(self.organism) - - super().__post_init__(**kwargs) - - -@dataclass -class ReactionDocument(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.ReactionDocument - class_class_curie: ClassVar[str] = "reaction:ReactionDocument" - class_name: ClassVar[str] = "ReactionDocument" - class_model_uri: ClassVar[URIRef] = REACTION.ReactionDocument - - genes: Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]] = empty_list() - reactions: Optional[Union[Dict[Union[str, ReactionId], Union[dict, Reaction]], List[Union[dict, Reaction]]]] = empty_dict() - gene_reaction_pairings: Optional[Union[Union[dict, "GeneReactionPairing"], List[Union[dict, "GeneReactionPairing"]]]] = empty_list() - organism: Optional[Union[str, OrganismId]] = None - has_evidence: Optional[Union[Union[str, EvidenceId], List[Union[str, EvidenceId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.genes, list): - self.genes = [self.genes] if self.genes is not None else [] - self.genes = [v if isinstance(v, GeneId) else GeneId(v) for v in self.genes] - - self._normalize_inlined_as_dict(slot_name="reactions", slot_type=Reaction, key_name="id", keyed=True) - - if not isinstance(self.gene_reaction_pairings, list): - self.gene_reaction_pairings = [self.gene_reaction_pairings] if self.gene_reaction_pairings is not None else [] - self.gene_reaction_pairings = [v if isinstance(v, GeneReactionPairing) else GeneReactionPairing(**as_dict(v)) for v in self.gene_reaction_pairings] - - if self.organism is not None and not isinstance(self.organism, OrganismId): - self.organism = OrganismId(self.organism) - - if not isinstance(self.has_evidence, list): - self.has_evidence = [self.has_evidence] if self.has_evidence is not None else [] - self.has_evidence = [v if isinstance(v, EvidenceId) else EvidenceId(v) for v in self.has_evidence] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = REACTION.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = REACTION.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Reaction(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.Reaction - class_class_curie: ClassVar[str] = "reaction:Reaction" - class_name: ClassVar[str] = "Reaction" - class_model_uri: ClassVar[URIRef] = REACTION.Reaction - - id: Union[str, ReactionId] = None - label: Optional[str] = None - description: Optional[str] = None - synonyms: Optional[Union[str, List[str]]] = empty_list() - subclass_of: Optional[Union[str, ReactionGroupingId]] = None - left_side: Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]] = empty_list() - right_side: Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ReactionId): - self.id = ReactionId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.synonyms, list): - self.synonyms = [self.synonyms] if self.synonyms is not None else [] - self.synonyms = [v if isinstance(v, str) else str(v) for v in self.synonyms] - - if self.subclass_of is not None and not isinstance(self.subclass_of, ReactionGroupingId): - self.subclass_of = ReactionGroupingId(self.subclass_of) - - if not isinstance(self.left_side, list): - self.left_side = [self.left_side] if self.left_side is not None else [] - self.left_side = [v if isinstance(v, ChemicalEntityId) else ChemicalEntityId(v) for v in self.left_side] - - if not isinstance(self.right_side, list): - self.right_side = [self.right_side] if self.right_side is not None else [] - self.right_side = [v if isinstance(v, ChemicalEntityId) else ChemicalEntityId(v) for v in self.right_side] - - super().__post_init__(**kwargs) - - -@dataclass -class ReactionGrouping(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.ReactionGrouping - class_class_curie: ClassVar[str] = "reaction:ReactionGrouping" - class_name: ClassVar[str] = "ReactionGrouping" - class_model_uri: ClassVar[URIRef] = REACTION.ReactionGrouping - - id: Union[str, ReactionGroupingId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ReactionGroupingId): - self.id = ReactionGroupingId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class ChemicalEntity(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.ChemicalEntity - class_class_curie: ClassVar[str] = "reaction:ChemicalEntity" - class_name: ClassVar[str] = "ChemicalEntity" - class_model_uri: ClassVar[URIRef] = REACTION.ChemicalEntity - - id: Union[str, ChemicalEntityId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ChemicalEntityId): - self.id = ChemicalEntityId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Evidence(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.Evidence - class_class_curie: ClassVar[str] = "reaction:Evidence" - class_name: ClassVar[str] = "Evidence" - class_model_uri: ClassVar[URIRef] = REACTION.Evidence - - id: Union[str, EvidenceId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, EvidenceId): - self.id = EvidenceId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.Gene - class_class_curie: ClassVar[str] = "reaction:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = REACTION.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Organism(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.Organism - class_class_curie: ClassVar[str] = "reaction:Organism" - class_name: ClassVar[str] = "Organism" - class_model_uri: ClassVar[URIRef] = REACTION.Organism - - id: Union[str, OrganismId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, OrganismId): - self.id = OrganismId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = REACTION.CompoundExpression - - -@dataclass -class GeneReactionPairing(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = REACTION.GeneReactionPairing - class_class_curie: ClassVar[str] = "reaction:GeneReactionPairing" - class_name: ClassVar[str] = "GeneReactionPairing" - class_model_uri: ClassVar[URIRef] = REACTION.GeneReactionPairing - - gene: Optional[Union[str, GeneId]] = None - reaction: Optional[Union[str, ReactionId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.gene is not None and not isinstance(self.gene, GeneId): - self.gene = GeneId(self.gene) - - if self.reaction is not None and not isinstance(self.reaction, ReactionId): - self.reaction = ReactionId(self.reaction) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = REACTION.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = REACTION.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = REACTION.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = REACTION.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = REACTION.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.reaction__label = Slot(uri=REACTION.label, name="reaction__label", curie=REACTION.curie('label'), - model_uri=REACTION.reaction__label, domain=None, range=Optional[str]) - -slots.reaction__description = Slot(uri=REACTION.description, name="reaction__description", curie=REACTION.curie('description'), - model_uri=REACTION.reaction__description, domain=None, range=Optional[str]) - -slots.reaction__synonyms = Slot(uri=REACTION.synonyms, name="reaction__synonyms", curie=REACTION.curie('synonyms'), - model_uri=REACTION.reaction__synonyms, domain=None, range=Optional[Union[str, List[str]]]) - -slots.reaction__subclass_of = Slot(uri=REACTION.subclass_of, name="reaction__subclass_of", curie=REACTION.curie('subclass_of'), - model_uri=REACTION.reaction__subclass_of, domain=None, range=Optional[Union[str, ReactionGroupingId]]) - -slots.reaction__left_side = Slot(uri=REACTION.left_side, name="reaction__left_side", curie=REACTION.curie('left_side'), - model_uri=REACTION.reaction__left_side, domain=None, range=Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]]) - -slots.reaction__right_side = Slot(uri=REACTION.right_side, name="reaction__right_side", curie=REACTION.curie('right_side'), - model_uri=REACTION.reaction__right_side, domain=None, range=Optional[Union[Union[str, ChemicalEntityId], List[Union[str, ChemicalEntityId]]]]) - -slots.geneToReaction__gene = Slot(uri=REACTION.gene, name="geneToReaction__gene", curie=REACTION.curie('gene'), - model_uri=REACTION.geneToReaction__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneToReaction__reactions = Slot(uri=REACTION.reactions, name="geneToReaction__reactions", curie=REACTION.curie('reactions'), - model_uri=REACTION.geneToReaction__reactions, domain=None, range=Optional[Union[Dict[Union[str, ReactionId], Union[dict, Reaction]], List[Union[dict, Reaction]]]]) - -slots.geneToReaction__organism = Slot(uri=REACTION.organism, name="geneToReaction__organism", curie=REACTION.curie('organism'), - model_uri=REACTION.geneToReaction__organism, domain=None, range=Optional[Union[str, OrganismId]]) - -slots.reactionDocument__genes = Slot(uri=REACTION.genes, name="reactionDocument__genes", curie=REACTION.curie('genes'), - model_uri=REACTION.reactionDocument__genes, domain=None, range=Optional[Union[Union[str, GeneId], List[Union[str, GeneId]]]]) - -slots.reactionDocument__reactions = Slot(uri=REACTION.reactions, name="reactionDocument__reactions", curie=REACTION.curie('reactions'), - model_uri=REACTION.reactionDocument__reactions, domain=None, range=Optional[Union[Dict[Union[str, ReactionId], Union[dict, Reaction]], List[Union[dict, Reaction]]]]) - -slots.reactionDocument__gene_reaction_pairings = Slot(uri=REACTION.gene_reaction_pairings, name="reactionDocument__gene_reaction_pairings", curie=REACTION.curie('gene_reaction_pairings'), - model_uri=REACTION.reactionDocument__gene_reaction_pairings, domain=None, range=Optional[Union[Union[dict, GeneReactionPairing], List[Union[dict, GeneReactionPairing]]]]) - -slots.reactionDocument__organism = Slot(uri=REACTION.organism, name="reactionDocument__organism", curie=REACTION.curie('organism'), - model_uri=REACTION.reactionDocument__organism, domain=None, range=Optional[Union[str, OrganismId]]) - -slots.reactionDocument__has_evidence = Slot(uri=REACTION.has_evidence, name="reactionDocument__has_evidence", curie=REACTION.curie('has_evidence'), - model_uri=REACTION.reactionDocument__has_evidence, domain=None, range=Optional[Union[Union[str, EvidenceId], List[Union[str, EvidenceId]]]]) - -slots.geneReactionPairing__gene = Slot(uri=REACTION.gene, name="geneReactionPairing__gene", curie=REACTION.curie('gene'), - model_uri=REACTION.geneReactionPairing__gene, domain=None, range=Optional[Union[str, GeneId]]) - -slots.geneReactionPairing__reaction = Slot(uri=REACTION.reaction, name="geneReactionPairing__reaction", curie=REACTION.curie('reaction'), - model_uri=REACTION.geneReactionPairing__reaction, domain=None, range=Optional[Union[str, ReactionId]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=REACTION.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=REACTION.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=REACTION.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=REACTION.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=REACTION.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=REACTION.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=REACTION.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=REACTION.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=REACTION.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=REACTION.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=REACTION.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=REACTION.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=REACTION.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=REACTION.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=REACTION.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=REACTION.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=REACTION.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=REACTION.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=REACTION.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=REACTION.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=REACTION.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=REACTION.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=REACTION.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=REACTION.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=REACTION.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/reaction/shacl/reaction.shacl.ttl b/projects/reaction/shacl/reaction.shacl.ttl deleted file mode 100644 index 7acc24ba3..000000000 --- a/projects/reaction/shacl/reaction.shacl.ttl +++ /dev/null @@ -1,339 +0,0 @@ -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix reaction: <http://w3id.org/ontogpt/reaction/> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -reaction:GeneToReaction a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class reaction:Reaction ; - sh:description "semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path reaction:reactions ], - [ sh:class reaction:Gene ; - sh:description "name of the gene that catalyzes the reaction" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path reaction:gene ], - [ sh:class reaction:Organism ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path reaction:organism ] ; - sh:targetClass reaction:GeneToReaction . - -reaction:ReactionDocument a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class reaction:Evidence ; - sh:description "evidence for the reaction" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path reaction:has_evidence ], - [ sh:class reaction:Organism ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path reaction:organism ], - [ sh:class reaction:Gene ; - sh:description "semicolon separated list of genes that catalyzes the mentioned reactions" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path reaction:genes ], - [ sh:class reaction:GeneReactionPairing ; - sh:description "semicolon separated list of gene to reaction pairings" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path reaction:gene_reaction_pairings ], - [ sh:class reaction:Reaction ; - sh:description "semicolon separated list of reaction equations (e.g. A+B = C+D) catalyzed by the gene" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path reaction:reactions ] ; - sh:targetClass reaction:ReactionDocument . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -reaction:Evidence a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass reaction:Evidence . - -reaction:GeneReactionPairing a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class reaction:Reaction ; - sh:description "equation describing the reaction (e.g. A+B = C+D) catalyzed by the gene" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path reaction:reaction ], - [ sh:class reaction:Gene ; - sh:description "name of the gene that catalyzes the reaction" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path reaction:gene ] ; - sh:targetClass reaction:GeneReactionPairing . - -reaction:ReactionGrouping a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass reaction:ReactionGrouping . - -reaction:ChemicalEntity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass reaction:ChemicalEntity . - -reaction:Organism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass reaction:Organism . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -reaction:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass reaction:Gene . - -reaction:Reaction a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class reaction:ReactionGrouping ; - sh:description "the category to which this biological process belongs" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path reaction:subclass_of ], - [ sh:class reaction:ChemicalEntity ; - sh:description "semicolon separated list of chemical entities on the right side" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path reaction:right_side ], - [ sh:description "alternative names of the reaction" ; - sh:order 2 ; - sh:path reaction:synonyms ], - [ sh:class reaction:ChemicalEntity ; - sh:description "semicolon separated list of chemical entities on the left side" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path reaction:left_side ], - [ sh:description "the name of the reaction" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path reaction:label ], - [ sh:description "a textual description of the reaction" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path reaction:description ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass reaction:Reaction . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/reaction/shex/reaction.shex b/projects/reaction/shex/reaction.shex deleted file mode 100644 index 636748acd..000000000 --- a/projects/reaction/shex/reaction.shex +++ /dev/null @@ -1,220 +0,0 @@ -BASE <http://w3id.org/ontogpt/reaction/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -<ChemicalEntity> CLOSED { - ( $<ChemicalEntity_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <ChemicalEntity> ] - ) -} - -core:CompoundExpression ( - @<GeneReactionPairing> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -<Evidence> CLOSED { - ( $<Evidence_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Evidence> ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<Gene> CLOSED { - ( $<Gene_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Gene> ] - ) -} - -<GeneReactionPairing> CLOSED { - ( $<GeneReactionPairing_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <gene> @<Gene> ? ; - <reaction> @<Reaction> ? - ) ; - rdf:type [ <GeneReactionPairing> ] ? - ) -} - -<GeneToReaction> CLOSED { - ( $<GeneToReaction_tes> ( <gene> @<Gene> ? ; - <reactions> @<Reaction> * ; - <organism> @<Organism> ? - ) ; - rdf:type [ <GeneToReaction> ] ? - ) -} - -core:NamedEntity ( - @<ChemicalEntity> OR @<Evidence> OR @<Gene> OR @<Organism> OR @<Reaction> OR @<ReactionGrouping> OR @core:RelationshipType -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -<Organism> CLOSED { - ( $<Organism_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Organism> ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -<Reaction> CLOSED { - ( $<Reaction_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? ; - <label> @linkml:String ? ; - <description> @linkml:String ? ; - <synonyms> @linkml:String * ; - <subclass_of> @<ReactionGrouping> ? ; - <left_side> @<ChemicalEntity> * ; - <right_side> @<ChemicalEntity> * - ) ; - rdf:type [ <Reaction> ] - ) -} - -<ReactionDocument> CLOSED { - ( $<ReactionDocument_tes> ( <genes> @<Gene> * ; - <reactions> @<Reaction> * ; - <gene_reaction_pairings> @<GeneReactionPairing> * ; - <organism> @<Organism> ? ; - <has_evidence> @<Evidence> * - ) ; - rdf:type [ <ReactionDocument> ] ? - ) -} - -<ReactionGrouping> CLOSED { - ( $<ReactionGrouping_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <ReactionGrouping> ] - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/reaction/sqlschema/reaction.sql b/projects/reaction/sqlschema/reaction.sql deleted file mode 100644 index 8fcc91b84..000000000 --- a/projects/reaction/sqlschema/reaction.sql +++ /dev/null @@ -1,115 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ChemicalEntity" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Evidence" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Organism" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "ReactionGrouping" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "GeneToReaction" ( - gene TEXT, - reactions TEXT, - organism TEXT, - PRIMARY KEY (gene, reactions, organism), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(organism) REFERENCES "Organism" (id) -); - -CREATE TABLE "Reaction" ( - id TEXT NOT NULL, - label TEXT, - description TEXT, - subclass_of TEXT, - left_side TEXT, - right_side TEXT, - PRIMARY KEY (id), - FOREIGN KEY(subclass_of) REFERENCES "ReactionGrouping" (id) -); - -CREATE TABLE "ReactionDocument" ( - genes TEXT, - reactions TEXT, - gene_reaction_pairings TEXT, - organism TEXT, - has_evidence TEXT, - PRIMARY KEY (genes, reactions, gene_reaction_pairings, organism, has_evidence), - FOREIGN KEY(organism) REFERENCES "Organism" (id) -); - -CREATE TABLE "GeneReactionPairing" ( - gene TEXT, - reaction TEXT, - PRIMARY KEY (gene, reaction), - FOREIGN KEY(gene) REFERENCES "Gene" (id), - FOREIGN KEY(reaction) REFERENCES "Reaction" (id) -); - -CREATE TABLE "Reaction_synonyms" ( - backref_id TEXT, - synonyms TEXT, - PRIMARY KEY (backref_id, synonyms), - FOREIGN KEY(backref_id) REFERENCES "Reaction" (id) -); diff --git a/projects/recipe/docs/Action.md b/projects/recipe/docs/Action.md deleted file mode 100644 index cb73e2e8f..000000000 --- a/projects/recipe/docs/Action.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: Action - - - - -URI: [recipe:Action](http://w3id.org/ontogpt/recipe/Action) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Step]-%20action%200..1>[Action|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Action],[Step])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[Step]-%20action%200..1>[Action|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Action],[Step]) - -## Identifier prefixes - - * dbpediaont - * FOODON - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞action](step__action.md)* <sub>0..1</sub> **[Action](Action.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/AnnotatorResult.md b/projects/recipe/docs/AnnotatorResult.md deleted file mode 100644 index 159a54e4b..000000000 --- a/projects/recipe/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [recipe:AnnotatorResult](http://w3id.org/ontogpt/recipe/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/Any.md b/projects/recipe/docs/Any.md deleted file mode 100644 index 8c087c31a..000000000 --- a/projects/recipe/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [recipe:Any](http://w3id.org/ontogpt/recipe/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/recipe/docs/CompoundExpression.md b/projects/recipe/docs/CompoundExpression.md deleted file mode 100644 index bd3d323a2..000000000 --- a/projects/recipe/docs/CompoundExpression.md +++ /dev/null @@ -1,24 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [recipe:CompoundExpression](http://w3id.org/ontogpt/recipe/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Step],[Quantity],[Ingredient],[FoodItem],[CompoundExpression]^-[Triple],[CompoundExpression]^-[Step],[CompoundExpression]^-[Quantity],[CompoundExpression]^-[Ingredient],[CompoundExpression]^-[FoodItem])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Step],[Quantity],[Ingredient],[FoodItem],[CompoundExpression]^-[Triple],[CompoundExpression]^-[Step],[CompoundExpression]^-[Quantity],[CompoundExpression]^-[Ingredient],[CompoundExpression]^-[FoodItem]) - -## Children - - * [FoodItem](FoodItem.md) - * [Ingredient](Ingredient.md) - * [Quantity](Quantity.md) - * [Step](Step.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/recipe/docs/ExtractionResult.md b/projects/recipe/docs/ExtractionResult.md deleted file mode 100644 index a21dd2caa..000000000 --- a/projects/recipe/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [recipe:ExtractionResult](http://w3id.org/ontogpt/recipe/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/recipe/docs/FoodItem.md b/projects/recipe/docs/FoodItem.md deleted file mode 100644 index 893fcb8c3..000000000 --- a/projects/recipe/docs/FoodItem.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: FoodItem - - - - -URI: [recipe:FoodItem](http://w3id.org/ontogpt/recipe/FoodItem) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[FoodType],[FoodType]<food%200..1-%20[FoodItem|state:string%20%3F],[Ingredient]++-%20food_item%200..1>[FoodItem],[Step]++-%20inputs%200..*>[FoodItem],[Step]++-%20outputs%200..*>[FoodItem],[CompoundExpression]^-[FoodItem],[Step],[Ingredient],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[FoodType],[FoodType]<food%200..1-%20[FoodItem|state:string%20%3F],[Ingredient]++-%20food_item%200..1>[FoodItem],[Step]++-%20inputs%200..*>[FoodItem],[Step]++-%20outputs%200..*>[FoodItem],[CompoundExpression]^-[FoodItem],[Step],[Ingredient],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞food_item](ingredient__food_item.md)* <sub>0..1</sub> **[FoodItem](FoodItem.md)** - * **None** *[➞inputs](step__inputs.md)* <sub>0..\*</sub> **[FoodItem](FoodItem.md)** - * **None** *[➞outputs](step__outputs.md)* <sub>0..\*</sub> **[FoodItem](FoodItem.md)** - -## Attributes - - -### Own - - * [➞food](foodItem__food.md) <sub>0..1</sub> - * Description: the food item - * Range: [FoodType](FoodType.md) - * [➞state](foodItem__state.md) <sub>0..1</sub> - * Description: the state of the food item (e.g. chopped, diced) - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/FoodType.md b/projects/recipe/docs/FoodType.md deleted file mode 100644 index 411873775..000000000 --- a/projects/recipe/docs/FoodType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: FoodType - - - - -URI: [recipe:FoodType](http://w3id.org/ontogpt/recipe/FoodType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[FoodItem]-%20food%200..1>[FoodType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[FoodType],[FoodItem])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[FoodItem]-%20food%200..1>[FoodType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[FoodType],[FoodItem]) - -## Identifier prefixes - - * dbpediaont - * FOODON - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞food](foodItem__food.md)* <sub>0..1</sub> **[FoodType](FoodType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/Ingredient.md b/projects/recipe/docs/Ingredient.md deleted file mode 100644 index 2abfcf2cf..000000000 --- a/projects/recipe/docs/Ingredient.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Class: Ingredient - - - - -URI: [recipe:Ingredient](http://w3id.org/ontogpt/recipe/Ingredient) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Quantity],[Quantity]<amount%200..1-++[Ingredient],[FoodItem]<food_item%200..1-++[Ingredient],[Recipe]++-%20ingredients%200..*>[Ingredient],[CompoundExpression]^-[Ingredient],[Recipe],[FoodItem],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Quantity],[Quantity]<amount%200..1-++[Ingredient],[FoodItem]<food_item%200..1-++[Ingredient],[Recipe]++-%20ingredients%200..*>[Ingredient],[CompoundExpression]^-[Ingredient],[Recipe],[FoodItem],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞ingredients](recipe__ingredients.md)* <sub>0..\*</sub> **[Ingredient](Ingredient.md)** - -## Attributes - - -### Own - - * [➞food_item](ingredient__food_item.md) <sub>0..1</sub> - * Description: the food item - * Range: [FoodItem](FoodItem.md) - * [➞amount](ingredient__amount.md) <sub>0..1</sub> - * Description: the quantity of the ingredient, e.g. 2 lbs - * Range: [Quantity](Quantity.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | FOODON:00004085 | - diff --git a/projects/recipe/docs/NamedEntity.md b/projects/recipe/docs/NamedEntity.md deleted file mode 100644 index e8cef3484..000000000 --- a/projects/recipe/docs/NamedEntity.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [recipe:NamedEntity](http://w3id.org/ontogpt/recipe/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[UtensilType],[Unit],[RelationshipType],[RecipeCategory],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[UtensilType],[NamedEntity]^-[Unit],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[RecipeCategory],[NamedEntity]^-[FoodType],[NamedEntity]^-[Action],[Triple],[FoodType],[Action])](https://yuml.me/diagram/nofunky;dir:TB/class/[UtensilType],[Unit],[RelationshipType],[RecipeCategory],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[UtensilType],[NamedEntity]^-[Unit],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[RecipeCategory],[NamedEntity]^-[FoodType],[NamedEntity]^-[Action],[Triple],[FoodType],[Action]) - -## Children - - * [Action](Action.md) - * [FoodType](FoodType.md) - * [RecipeCategory](RecipeCategory.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - * [UtensilType](UtensilType.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/NullDataOptions.md b/projects/recipe/docs/NullDataOptions.md deleted file mode 100644 index e1b6bd1a6..000000000 --- a/projects/recipe/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [recipe:NullDataOptions](http://w3id.org/ontogpt/recipe/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/recipe/docs/Publication.md b/projects/recipe/docs/Publication.md deleted file mode 100644 index aed8f8d74..000000000 --- a/projects/recipe/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [recipe:Publication](http://w3id.org/ontogpt/recipe/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/Quantity.md b/projects/recipe/docs/Quantity.md deleted file mode 100644 index fd676298c..000000000 --- a/projects/recipe/docs/Quantity.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Quantity - - - - -URI: [recipe:Quantity](http://w3id.org/ontogpt/recipe/Quantity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[Unit]<unit%200..1-%20[Quantity|value:string%20%3F],[Ingredient]++-%20amount%200..1>[Quantity],[CompoundExpression]^-[Quantity],[Ingredient],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Unit],[Unit]<unit%200..1-%20[Quantity|value:string%20%3F],[Ingredient]++-%20amount%200..1>[Quantity],[CompoundExpression]^-[Quantity],[Ingredient],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞amount](ingredient__amount.md)* <sub>0..1</sub> **[Quantity](Quantity.md)** - -## Attributes - - -### Own - - * [➞value](quantity__value.md) <sub>0..1</sub> - * Description: the value of the quantity - * Range: [String](types/String.md) - * [➞unit](quantity__unit.md) <sub>0..1</sub> - * Description: the unit of the quantity, e.g. grams, cups, etc. - * Range: [Unit](Unit.md) diff --git a/projects/recipe/docs/RecipeCategory.md b/projects/recipe/docs/RecipeCategory.md deleted file mode 100644 index 3a5ea90cf..000000000 --- a/projects/recipe/docs/RecipeCategory.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: RecipeCategory - - - - -URI: [recipe:RecipeCategory](http://w3id.org/ontogpt/recipe/RecipeCategory) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Recipe]-%20categories%200..*>[RecipeCategory|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RecipeCategory],[Recipe],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Recipe]-%20categories%200..*>[RecipeCategory|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RecipeCategory],[Recipe],[NamedEntity]) - -## Identifier prefixes - - * dbpediaont - * FOODON - * HANCESTRO - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞categories](recipe__categories.md)* <sub>0..\*</sub> **[RecipeCategory](RecipeCategory.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/RelationshipType.md b/projects/recipe/docs/RelationshipType.md deleted file mode 100644 index b73e48c48..000000000 --- a/projects/recipe/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [recipe:RelationshipType](http://w3id.org/ontogpt/recipe/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/Step.md b/projects/recipe/docs/Step.md deleted file mode 100644 index e3c5f94c5..000000000 --- a/projects/recipe/docs/Step.md +++ /dev/null @@ -1,43 +0,0 @@ - -# Class: Step - - - - -URI: [recipe:Step](http://w3id.org/ontogpt/recipe/Step) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[UtensilType],[UtensilType]<utensils%200..*-%20[Step],[FoodItem]<outputs%200..*-++[Step],[FoodItem]<inputs%200..*-++[Step],[Action]<action%200..1-%20[Step],[Recipe]++-%20steps%200..*>[Step],[CompoundExpression]^-[Step],[Recipe],[FoodItem],[CompoundExpression],[Action])](https://yuml.me/diagram/nofunky;dir:TB/class/[UtensilType],[UtensilType]<utensils%200..*-%20[Step],[FoodItem]<outputs%200..*-++[Step],[FoodItem]<inputs%200..*-++[Step],[Action]<action%200..1-%20[Step],[Recipe]++-%20steps%200..*>[Step],[CompoundExpression]^-[Step],[Recipe],[FoodItem],[CompoundExpression],[Action]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞steps](recipe__steps.md)* <sub>0..\*</sub> **[Step](Step.md)** - -## Attributes - - -### Own - - * [➞action](step__action.md) <sub>0..1</sub> - * Description: the action taken in this step (e.g. mix, add) - * Range: [Action](Action.md) - * [➞inputs](step__inputs.md) <sub>0..\*</sub> - * Description: a semicolon separated list of the inputs of this step - * Range: [FoodItem](FoodItem.md) - * [➞outputs](step__outputs.md) <sub>0..\*</sub> - * Description: a semicolon separated list of the outputs of this step - * Range: [FoodItem](FoodItem.md) - * [➞utensils](step__utensils.md) <sub>0..\*</sub> - * Description: the kitchen utensil used in this step (e.g. pan, bowl) - * Range: [UtensilType](UtensilType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | FOODON:00004087 | - diff --git a/projects/recipe/docs/TextWithTriples.md b/projects/recipe/docs/TextWithTriples.md deleted file mode 100644 index 97fc5bae1..000000000 --- a/projects/recipe/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [recipe:TextWithTriples](http://w3id.org/ontogpt/recipe/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/recipe/docs/Triple.md b/projects/recipe/docs/Triple.md deleted file mode 100644 index 7f1334410..000000000 --- a/projects/recipe/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [recipe:Triple](http://w3id.org/ontogpt/recipe/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/recipe/docs/Unit.md b/projects/recipe/docs/Unit.md deleted file mode 100644 index 203ea7914..000000000 --- a/projects/recipe/docs/Unit.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Class: Unit - - - - -URI: [recipe:Unit](http://w3id.org/ontogpt/recipe/Unit) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Quantity]-%20unit%200..1>[Unit|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Unit],[Quantity],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Quantity]-%20unit%200..1>[Unit|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Unit],[Quantity],[NamedEntity]) - -## Identifier prefixes - - * UO - * NCIT - * dbpediaont - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞unit](quantity__unit.md)* <sub>0..1</sub> **[Unit](Unit.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/UtensilType.md b/projects/recipe/docs/UtensilType.md deleted file mode 100644 index 2fcbadd98..000000000 --- a/projects/recipe/docs/UtensilType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: UtensilType - - - - -URI: [recipe:UtensilType](http://w3id.org/ontogpt/recipe/UtensilType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Step]-%20utensils%200..*>[UtensilType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[UtensilType],[Step],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Step]-%20utensils%200..*>[UtensilType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[UtensilType],[Step],[NamedEntity]) - -## Identifier prefixes - - * dbpediaont - * FOODON - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞utensils](step__utensils.md)* <sub>0..\*</sub> **[UtensilType](UtensilType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/recipe/docs/annotatorResult__object_id.md b/projects/recipe/docs/annotatorResult__object_id.md deleted file mode 100644 index 8f36a50fc..000000000 --- a/projects/recipe/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [recipe:annotatorResult__object_id](http://w3id.org/ontogpt/recipe/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/recipe/docs/annotatorResult__object_text.md b/projects/recipe/docs/annotatorResult__object_text.md deleted file mode 100644 index bbd4f7329..000000000 --- a/projects/recipe/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [recipe:annotatorResult__object_text](http://w3id.org/ontogpt/recipe/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/recipe/docs/annotatorResult__subject_text.md b/projects/recipe/docs/annotatorResult__subject_text.md deleted file mode 100644 index 90eb59580..000000000 --- a/projects/recipe/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [recipe:annotatorResult__subject_text](http://w3id.org/ontogpt/recipe/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/recipe/docs/extractionResult__extracted_object.md b/projects/recipe/docs/extractionResult__extracted_object.md deleted file mode 100644 index 73539d87c..000000000 --- a/projects/recipe/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [recipe:extractionResult__extracted_object](http://w3id.org/ontogpt/recipe/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/recipe/docs/extractionResult__input_id.md b/projects/recipe/docs/extractionResult__input_id.md deleted file mode 100644 index 37362b850..000000000 --- a/projects/recipe/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [recipe:extractionResult__input_id](http://w3id.org/ontogpt/recipe/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/recipe/docs/extractionResult__input_text.md b/projects/recipe/docs/extractionResult__input_text.md deleted file mode 100644 index 531648c15..000000000 --- a/projects/recipe/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [recipe:extractionResult__input_text](http://w3id.org/ontogpt/recipe/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/recipe/docs/extractionResult__input_title.md b/projects/recipe/docs/extractionResult__input_title.md deleted file mode 100644 index 6d2d20ebe..000000000 --- a/projects/recipe/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [recipe:extractionResult__input_title](http://w3id.org/ontogpt/recipe/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/recipe/docs/extractionResult__named_entities.md b/projects/recipe/docs/extractionResult__named_entities.md deleted file mode 100644 index 1a74a622c..000000000 --- a/projects/recipe/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [recipe:extractionResult__named_entities](http://w3id.org/ontogpt/recipe/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/recipe/docs/extractionResult__prompt.md b/projects/recipe/docs/extractionResult__prompt.md deleted file mode 100644 index 7c1a6a917..000000000 --- a/projects/recipe/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [recipe:extractionResult__prompt](http://w3id.org/ontogpt/recipe/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/recipe/docs/extractionResult__raw_completion_output.md b/projects/recipe/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 6a73aaa9b..000000000 --- a/projects/recipe/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [recipe:extractionResult__raw_completion_output](http://w3id.org/ontogpt/recipe/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/recipe/docs/foodItem__food.md b/projects/recipe/docs/foodItem__food.md deleted file mode 100644 index 74f5826a7..000000000 --- a/projects/recipe/docs/foodItem__food.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: food - - -the food item - -URI: [recipe:foodItem__food](http://w3id.org/ontogpt/recipe/foodItem__food) - - -## Domain and Range - -None → <sub>0..1</sub> [FoodType](FoodType.md) - -## Parents - - -## Children - - -## Used by - - * [FoodItem](FoodItem.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | BFO:0000051 | - diff --git a/projects/recipe/docs/foodItem__state.md b/projects/recipe/docs/foodItem__state.md deleted file mode 100644 index d09bfc6a6..000000000 --- a/projects/recipe/docs/foodItem__state.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: state - - -the state of the food item (e.g. chopped, diced) - -URI: [recipe:foodItem__state](http://w3id.org/ontogpt/recipe/foodItem__state) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [FoodItem](FoodItem.md) diff --git a/projects/recipe/docs/ingredient__amount.md b/projects/recipe/docs/ingredient__amount.md deleted file mode 100644 index a7e0a01e1..000000000 --- a/projects/recipe/docs/ingredient__amount.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: amount - - -the quantity of the ingredient, e.g. 2 lbs - -URI: [recipe:ingredient__amount](http://w3id.org/ontogpt/recipe/ingredient__amount) - - -## Domain and Range - -None → <sub>0..1</sub> [Quantity](Quantity.md) - -## Parents - - -## Children - - -## Used by - - * [Ingredient](Ingredient.md) diff --git a/projects/recipe/docs/ingredient__food_item.md b/projects/recipe/docs/ingredient__food_item.md deleted file mode 100644 index 5d9ec1c7d..000000000 --- a/projects/recipe/docs/ingredient__food_item.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: food_item - - -the food item - -URI: [recipe:ingredient__food_item](http://w3id.org/ontogpt/recipe/ingredient__food_item) - - -## Domain and Range - -None → <sub>0..1</sub> [FoodItem](FoodItem.md) - -## Parents - - -## Children - - -## Used by - - * [Ingredient](Ingredient.md) diff --git a/projects/recipe/docs/namedEntity__id.md b/projects/recipe/docs/namedEntity__id.md deleted file mode 100644 index d5de30f9b..000000000 --- a/projects/recipe/docs/namedEntity__id.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [recipe:namedEntity__id](http://w3id.org/ontogpt/recipe/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Action](Action.md) - * [FoodType](FoodType.md) - * [NamedEntity](NamedEntity.md) - * [RecipeCategory](RecipeCategory.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - * [UtensilType](UtensilType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/recipe/docs/namedEntity__label.md b/projects/recipe/docs/namedEntity__label.md deleted file mode 100644 index 1a4979d25..000000000 --- a/projects/recipe/docs/namedEntity__label.md +++ /dev/null @@ -1,36 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [recipe:namedEntity__label](http://w3id.org/ontogpt/recipe/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Action](Action.md) - * [FoodType](FoodType.md) - * [NamedEntity](NamedEntity.md) - * [RecipeCategory](RecipeCategory.md) - * [RelationshipType](RelationshipType.md) - * [Unit](Unit.md) - * [UtensilType](UtensilType.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/recipe/docs/publication__abstract.md b/projects/recipe/docs/publication__abstract.md deleted file mode 100644 index 02fe69c28..000000000 --- a/projects/recipe/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [recipe:publication__abstract](http://w3id.org/ontogpt/recipe/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/recipe/docs/publication__combined_text.md b/projects/recipe/docs/publication__combined_text.md deleted file mode 100644 index 35f1aae56..000000000 --- a/projects/recipe/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [recipe:publication__combined_text](http://w3id.org/ontogpt/recipe/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/recipe/docs/publication__full_text.md b/projects/recipe/docs/publication__full_text.md deleted file mode 100644 index 19d1c161a..000000000 --- a/projects/recipe/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [recipe:publication__full_text](http://w3id.org/ontogpt/recipe/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/recipe/docs/publication__id.md b/projects/recipe/docs/publication__id.md deleted file mode 100644 index 08c4bc8e2..000000000 --- a/projects/recipe/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [recipe:publication__id](http://w3id.org/ontogpt/recipe/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/recipe/docs/publication__title.md b/projects/recipe/docs/publication__title.md deleted file mode 100644 index 38963c34a..000000000 --- a/projects/recipe/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [recipe:publication__title](http://w3id.org/ontogpt/recipe/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/recipe/docs/quantity__unit.md b/projects/recipe/docs/quantity__unit.md deleted file mode 100644 index e69c68805..000000000 --- a/projects/recipe/docs/quantity__unit.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: unit - - -the unit of the quantity, e.g. grams, cups, etc. - -URI: [recipe:quantity__unit](http://w3id.org/ontogpt/recipe/quantity__unit) - - -## Domain and Range - -None → <sub>0..1</sub> [Unit](Unit.md) - -## Parents - - -## Children - - -## Used by - - * [Quantity](Quantity.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | qudt:unit | - diff --git a/projects/recipe/docs/quantity__value.md b/projects/recipe/docs/quantity__value.md deleted file mode 100644 index 2a5d28a3a..000000000 --- a/projects/recipe/docs/quantity__value.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: value - - -the value of the quantity - -URI: [recipe:quantity__value](http://w3id.org/ontogpt/recipe/quantity__value) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Quantity](Quantity.md) diff --git a/projects/recipe/docs/recipe.md b/projects/recipe/docs/recipe.md deleted file mode 100644 index c9f5c6960..000000000 --- a/projects/recipe/docs/recipe.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: Recipe - - - - -URI: [recipe:Recipe](http://w3id.org/ontogpt/recipe/Recipe) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Step],[RecipeCategory],[Step]<steps%200..*-++[Recipe|url:uriorcurie;label:string%20%3F;description:string%20%3F],[Ingredient]<ingredients%200..*-++[Recipe],[RecipeCategory]<categories%200..*-%20[Recipe],[Ingredient])](https://yuml.me/diagram/nofunky;dir:TB/class/[Step],[RecipeCategory],[Step]<steps%200..*-++[Recipe|url:uriorcurie;label:string%20%3F;description:string%20%3F],[Ingredient]<ingredients%200..*-++[Recipe],[RecipeCategory]<categories%200..*-%20[Recipe],[Ingredient]) - -## Attributes - - -### Own - - * [➞url](recipe__url.md) <sub>1..1</sub> - * Range: [Uriorcurie](types/Uriorcurie.md) - * [➞label](recipe__label.md) <sub>0..1</sub> - * Description: the name of the recipe - * Range: [String](types/String.md) - * [➞description](recipe__description.md) <sub>0..1</sub> - * Description: a brief textual description of the recipe - * Range: [String](types/String.md) - * [➞categories](recipe__categories.md) <sub>0..\*</sub> - * Description: a semicolon separated list of the categories to which this recipe belongs - * Range: [RecipeCategory](RecipeCategory.md) - * [➞ingredients](recipe__ingredients.md) <sub>0..\*</sub> - * Description: a semicolon separated list of the ingredients plus quantities of the recipe - * Range: [Ingredient](Ingredient.md) - * [➞steps](recipe__steps.md) <sub>0..\*</sub> - * Description: a semicolon separated list of the individual steps involved in this recipe - * Range: [Step](Step.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | FOODON:00004081 | - diff --git a/projects/recipe/docs/recipe__categories.md b/projects/recipe/docs/recipe__categories.md deleted file mode 100644 index 552d36f1a..000000000 --- a/projects/recipe/docs/recipe__categories.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: categories - - -a semicolon separated list of the categories to which this recipe belongs - -URI: [recipe:recipe__categories](http://w3id.org/ontogpt/recipe/recipe__categories) - - -## Domain and Range - -None → <sub>0..\*</sub> [RecipeCategory](RecipeCategory.md) - -## Parents - - -## Children - - -## Used by - - * [Recipe](Recipe.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | dcterms:subject | - diff --git a/projects/recipe/docs/recipe__description.md b/projects/recipe/docs/recipe__description.md deleted file mode 100644 index 9f8902a2a..000000000 --- a/projects/recipe/docs/recipe__description.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: description - - -a brief textual description of the recipe - -URI: [recipe:recipe__description](http://w3id.org/ontogpt/recipe/recipe__description) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Recipe](Recipe.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | dcterms:description | - diff --git a/projects/recipe/docs/recipe__ingredients.md b/projects/recipe/docs/recipe__ingredients.md deleted file mode 100644 index fd33e366b..000000000 --- a/projects/recipe/docs/recipe__ingredients.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: ingredients - - -a semicolon separated list of the ingredients plus quantities of the recipe - -URI: [recipe:recipe__ingredients](http://w3id.org/ontogpt/recipe/recipe__ingredients) - - -## Domain and Range - -None → <sub>0..\*</sub> [Ingredient](Ingredient.md) - -## Parents - - -## Children - - -## Used by - - * [Recipe](Recipe.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | FOODON:00002420 | - diff --git a/projects/recipe/docs/recipe__label.md b/projects/recipe/docs/recipe__label.md deleted file mode 100644 index dfc9b8edc..000000000 --- a/projects/recipe/docs/recipe__label.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: label - - -the name of the recipe - -URI: [recipe:recipe__label](http://w3id.org/ontogpt/recipe/recipe__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Recipe](Recipe.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | rdfs:label | - diff --git a/projects/recipe/docs/recipe__steps.md b/projects/recipe/docs/recipe__steps.md deleted file mode 100644 index eb00df9a4..000000000 --- a/projects/recipe/docs/recipe__steps.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: steps - - -a semicolon separated list of the individual steps involved in this recipe - -URI: [recipe:recipe__steps](http://w3id.org/ontogpt/recipe/recipe__steps) - - -## Domain and Range - -None → <sub>0..\*</sub> [Step](Step.md) - -## Parents - - -## Children - - -## Used by - - * [Recipe](Recipe.md) diff --git a/projects/recipe/docs/recipe__url.md b/projects/recipe/docs/recipe__url.md deleted file mode 100644 index c0f59c5bf..000000000 --- a/projects/recipe/docs/recipe__url.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: url - - - - -URI: [recipe:recipe__url](http://w3id.org/ontogpt/recipe/recipe__url) - - -## Domain and Range - -None → <sub>1..1</sub> [Uriorcurie](types/Uriorcurie.md) - -## Parents - - -## Children - - -## Used by - - * [Recipe](Recipe.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | rdf:Resource | - diff --git a/projects/recipe/docs/step__action.md b/projects/recipe/docs/step__action.md deleted file mode 100644 index cc3e9b6d4..000000000 --- a/projects/recipe/docs/step__action.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: action - - -the action taken in this step (e.g. mix, add) - -URI: [recipe:step__action](http://w3id.org/ontogpt/recipe/step__action) - - -## Domain and Range - -None → <sub>0..1</sub> [Action](Action.md) - -## Parents - - -## Children - - -## Used by - - * [Step](Step.md) diff --git a/projects/recipe/docs/step__inputs.md b/projects/recipe/docs/step__inputs.md deleted file mode 100644 index 938b74117..000000000 --- a/projects/recipe/docs/step__inputs.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: inputs - - -a semicolon separated list of the inputs of this step - -URI: [recipe:step__inputs](http://w3id.org/ontogpt/recipe/step__inputs) - - -## Domain and Range - -None → <sub>0..\*</sub> [FoodItem](FoodItem.md) - -## Parents - - -## Children - - -## Used by - - * [Step](Step.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | RO:0002233 | - diff --git a/projects/recipe/docs/step__outputs.md b/projects/recipe/docs/step__outputs.md deleted file mode 100644 index 4384ff660..000000000 --- a/projects/recipe/docs/step__outputs.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: outputs - - -a semicolon separated list of the outputs of this step - -URI: [recipe:step__outputs](http://w3id.org/ontogpt/recipe/step__outputs) - - -## Domain and Range - -None → <sub>0..\*</sub> [FoodItem](FoodItem.md) - -## Parents - - -## Children - - -## Used by - - * [Step](Step.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | RO:0002234 | - diff --git a/projects/recipe/docs/step__utensils.md b/projects/recipe/docs/step__utensils.md deleted file mode 100644 index 584f6084e..000000000 --- a/projects/recipe/docs/step__utensils.md +++ /dev/null @@ -1,29 +0,0 @@ - -# Slot: utensils - - -the kitchen utensil used in this step (e.g. pan, bowl) - -URI: [recipe:step__utensils](http://w3id.org/ontogpt/recipe/step__utensils) - - -## Domain and Range - -None → <sub>0..\*</sub> [UtensilType](UtensilType.md) - -## Parents - - -## Children - - -## Used by - - * [Step](Step.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | RO:0002500 | - diff --git a/projects/recipe/docs/textWithTriples__publication.md b/projects/recipe/docs/textWithTriples__publication.md deleted file mode 100644 index 2056033ae..000000000 --- a/projects/recipe/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [recipe:textWithTriples__publication](http://w3id.org/ontogpt/recipe/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/recipe/docs/textWithTriples__triples.md b/projects/recipe/docs/textWithTriples__triples.md deleted file mode 100644 index acbc04e65..000000000 --- a/projects/recipe/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [recipe:textWithTriples__triples](http://w3id.org/ontogpt/recipe/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/recipe/docs/triple__object.md b/projects/recipe/docs/triple__object.md deleted file mode 100644 index 7669b81f3..000000000 --- a/projects/recipe/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [recipe:triple__object](http://w3id.org/ontogpt/recipe/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/recipe/docs/triple__object_qualifier.md b/projects/recipe/docs/triple__object_qualifier.md deleted file mode 100644 index f2b4a904d..000000000 --- a/projects/recipe/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [recipe:triple__object_qualifier](http://w3id.org/ontogpt/recipe/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/recipe/docs/triple__predicate.md b/projects/recipe/docs/triple__predicate.md deleted file mode 100644 index d4264ec18..000000000 --- a/projects/recipe/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [recipe:triple__predicate](http://w3id.org/ontogpt/recipe/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/recipe/docs/triple__qualifier.md b/projects/recipe/docs/triple__qualifier.md deleted file mode 100644 index 8f0dcdb4c..000000000 --- a/projects/recipe/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [recipe:triple__qualifier](http://w3id.org/ontogpt/recipe/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/recipe/docs/triple__subject.md b/projects/recipe/docs/triple__subject.md deleted file mode 100644 index 07ec2df93..000000000 --- a/projects/recipe/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [recipe:triple__subject](http://w3id.org/ontogpt/recipe/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/recipe/docs/triple__subject_qualifier.md b/projects/recipe/docs/triple__subject_qualifier.md deleted file mode 100644 index 9cfc7a442..000000000 --- a/projects/recipe/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [recipe:triple__subject_qualifier](http://w3id.org/ontogpt/recipe/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/recipe/docs/types/Boolean.md b/projects/recipe/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/recipe/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/recipe/docs/types/Curie.md b/projects/recipe/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/recipe/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/recipe/docs/types/Date.md b/projects/recipe/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/recipe/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/recipe/docs/types/DateOrDatetime.md b/projects/recipe/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/recipe/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/recipe/docs/types/Datetime.md b/projects/recipe/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/recipe/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/recipe/docs/types/Decimal.md b/projects/recipe/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/recipe/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/recipe/docs/types/Double.md b/projects/recipe/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/recipe/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/recipe/docs/types/Float.md b/projects/recipe/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/recipe/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/recipe/docs/types/Integer.md b/projects/recipe/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/recipe/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/recipe/docs/types/Jsonpath.md b/projects/recipe/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/recipe/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/recipe/docs/types/Jsonpointer.md b/projects/recipe/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/recipe/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/recipe/docs/types/Ncname.md b/projects/recipe/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/recipe/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/recipe/docs/types/Nodeidentifier.md b/projects/recipe/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/recipe/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/recipe/docs/types/Objectidentifier.md b/projects/recipe/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/recipe/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/recipe/docs/types/Sparqlpath.md b/projects/recipe/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/recipe/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/recipe/docs/types/String.md b/projects/recipe/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/recipe/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/recipe/docs/types/Time.md b/projects/recipe/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/recipe/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/recipe/docs/types/Uri.md b/projects/recipe/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/recipe/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/recipe/docs/types/Uriorcurie.md b/projects/recipe/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/recipe/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/recipe/excel/recipe.xlsx b/projects/recipe/excel/recipe.xlsx deleted file mode 100644 index b3874b666b1c08b4c3e64e9cd5a54121b91aa16d..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 12064 zcmeHtbyU>t);8VU(nyMcNVjy#(A@~aNT;-PcPi2;CEeZKNDUp*N=e5%;yK4hKAyAA zAK$y)e-3NS46_#d;{IK`_r2w1pkZ(zARrJRkksJS#5G${yusf}!7mK(%gE}LyseeB z-7^DgYbGZPbJ=iN<Thpu(Oc=Qc}taj^5^6enM=K{lAIioMk0=WS8htJ5g@(==FmFa 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z|7PYlN)<R=KJY|$y}^Hu@(jFf`T)w^ZO?y>@(Jrfl)I~o{~Uz^>=F;0<!%oD?@)dY z5B~Y%>6M84Aj<Q*q4Is0`!mtsFgW-R!`w|s@59_52>yoA1uwEZ@J!DiG~fFpsoyY^ z-~{&&%!Bs(SDX2hn=GP-VIDN#`%{A7ry(VI80J9>zTeRPhN&Zc80J9}zTb`g3kFh@ z{0`=KZ+2fh_lxP@qAidAD6Q`c-Y-sn3+7S&>*)V1RqqSmFHe38uTkF#|4p%SALo9O h{*6NeUWa}lWy{OJf_J5Vu22y`=z)JLp!@mle*lm<Q#Swr diff --git a/projects/recipe/graphql/recipe.graphql b/projects/recipe/graphql/recipe.graphql deleted file mode 100644 index f13d1b830..000000000 --- a/projects/recipe/graphql/recipe.graphql +++ /dev/null @@ -1,129 +0,0 @@ -type Action - { - id: String! - label: String - } - -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type FoodItem - { - food: FoodType - state: String - } - -type FoodType - { - id: String! - label: String - } - -type Ingredient - { - foodItem: FoodItem - amount: Quantity - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type Quantity - { - value: String - unit: Unit - } - -type Recipe - { - url: Uriorcurie! - label: String - description: String - categories: [RecipeCategory] - ingredients: [Ingredient] - steps: [Step] - } - -type RecipeCategory - { - id: String! - label: String - } - -type RelationshipType - { - id: String! - label: String - } - -type Step - { - action: Action - inputs: [FoodItem] - outputs: [FoodItem] - utensils: [UtensilType] - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - -type Unit - { - id: String! - label: String - } - -type UtensilType - { - id: String! - label: String - } - diff --git a/projects/recipe/jsonld/recipe.context.jsonld b/projects/recipe/jsonld/recipe.context.jsonld deleted file mode 100644 index 552c39b04..000000000 --- a/projects/recipe/jsonld/recipe.context.jsonld +++ /dev/null @@ -1,201 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:56:08", - "source": "recipe.yaml" - }, - "@context": { - "AUTO": "http://example.org/auto/", - "BFO": { - "@id": "http://purl.obolibrary.org/obo/BFO_", - "@prefix": true - }, - "FOODON": { - "@id": "http://purl.obolibrary.org/obo/FOODON_", - "@prefix": true - }, - "HANCESTRO": { - "@id": "http://purl.obolibrary.org/obo/HANCESTRO_", - "@prefix": true - }, - "NCIT": { - "@id": "http://purl.obolibrary.org/obo/NCIT_", - "@prefix": true - }, - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "UO": { - "@id": "http://purl.obolibrary.org/obo/UO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "dbpediaont": "http://dbpedia.org/ontology/", - "dcterms": "http://purl.org/dc/terms/", - "linkml": "https://w3id.org/linkml/", - "qudt": "http://qudt.org/schema/qudt/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "recipe": "http://w3id.org/ontogpt/recipe/", - "@vocab": "http://w3id.org/ontogpt/recipe/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "food": { - "@type": "@id", - "@id": "BFO:0000051" - }, - "amount": { - "@type": "@id" - }, - "food_item": { - "@type": "@id" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "unit": { - "@type": "@id", - "@id": "qudt:unit" - }, - "categories": { - "@type": "@id", - "@id": "dcterms:subject" - }, - "description": { - "@id": "dcterms:description" - }, - "ingredients": { - "@type": "@id", - "@id": "FOODON:00002420" - }, - "steps": { - "@type": "@id" - }, - "url": "@id", - "action": { - "@type": "@id" - }, - "inputs": { - "@type": "@id", - "@id": "RO:0002233" - }, - "outputs": { - "@type": "@id", - "@id": "RO:0002234" - }, - "utensils": { - "@type": "@id", - "@id": "RO:0002500" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "Ingredient": { - "@id": "FOODON:00004085" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "Step": { - "@id": "FOODON:00004087" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/recipe/jsonld/recipe.jsonld b/projects/recipe/jsonld/recipe.jsonld deleted file mode 100644 index 0ef266f0a..000000000 --- a/projects/recipe/jsonld/recipe.jsonld +++ /dev/null @@ -1,1828 +0,0 @@ -{ - "name": "recipe-template", - "description": "A template for food recipes", - "title": "Food Recipe Template", - "id": "https://w3id.org/ontogpt/recipe", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "recipe", - "prefix_reference": "http://w3id.org/ontogpt/recipe/" - }, - { - "prefix_prefix": "FOODON", - "prefix_reference": "http://purl.obolibrary.org/obo/FOODON_" - }, - { - "prefix_prefix": "UO", - "prefix_reference": "http://purl.obolibrary.org/obo/UO_" - }, - { - "prefix_prefix": "dcterms", - "prefix_reference": "http://purl.org/dc/terms/" - }, - { - "prefix_prefix": "HANCESTRO", - "prefix_reference": "http://purl.obolibrary.org/obo/HANCESTRO_" - }, - { - "prefix_prefix": "BFO", - "prefix_reference": "http://purl.obolibrary.org/obo/BFO_" - }, - { - "prefix_prefix": "AUTO", - "prefix_reference": "http://example.org/auto/" - }, - { - "prefix_prefix": "RO", - "prefix_reference": "http://purl.obolibrary.org/obo/RO_" - }, - { - "prefix_prefix": "qudt", - "prefix_reference": "http://qudt.org/schema/qudt/" - }, - { - "prefix_prefix": "dbpediaont", - "prefix_reference": "http://dbpedia.org/ontology/" - } - ], - "default_prefix": "recipe", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "recipe__url", - "annotations": [ - { - "tag": "prompt.ignore", - "value": "True", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://example.org/UNKNOWN/rdf/Resource" - ], - "slot_uri": "http://example.org/UNKNOWN/rdf/Resource", - "identifier": true, - "alias": "url", - "owner": "Recipe", - "domain_of": [ - "Recipe" - ], - "range": "uriorcurie", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "recipe__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "the name of the recipe", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "Recipe", - "domain_of": [ - "Recipe" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "recipe__description", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "a brief textual description of the recipe", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://purl.org/dc/terms/description" - ], - "slot_uri": "http://purl.org/dc/terms/description", - "alias": "description", - "owner": "Recipe", - "domain_of": [ - "Recipe" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "recipe__categories", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the categories to which this recipe belongs", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://purl.org/dc/terms/subject" - ], - "slot_uri": "http://purl.org/dc/terms/subject", - "multivalued": true, - "alias": "categories", - "owner": "Recipe", - "domain_of": [ - "Recipe" - ], - "range": "RecipeCategory", - "@type": "SlotDefinition" - }, - { - "name": "recipe__ingredients", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the ingredients plus quantities of the recipe", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://purl.obolibrary.org/obo/FOODON_00002420" - ], - "slot_uri": "http://purl.obolibrary.org/obo/FOODON_00002420", - "multivalued": true, - "alias": "ingredients", - "owner": "Recipe", - "domain_of": [ - "Recipe" - ], - "range": "Ingredient", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "recipe__steps", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the individual steps involved in this recipe", - "from_schema": "https://w3id.org/ontogpt/recipe", - "slot_uri": "http://w3id.org/ontogpt/recipe/steps", - "multivalued": true, - "alias": "steps", - "owner": "Recipe", - "domain_of": [ - "Recipe" - ], - "range": "Step", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "ingredient__food_item", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the food item", - "from_schema": "https://w3id.org/ontogpt/recipe", - "slot_uri": "http://w3id.org/ontogpt/recipe/food_item", - "alias": "food_item", - "owner": "Ingredient", - "domain_of": [ - "Ingredient" - ], - "range": "FoodItem", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "ingredient__amount", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the quantity of the ingredient, e.g. 2 lbs", - "from_schema": "https://w3id.org/ontogpt/recipe", - "slot_uri": "http://w3id.org/ontogpt/recipe/amount", - "alias": "amount", - "owner": "Ingredient", - "domain_of": [ - "Ingredient" - ], - "range": "Quantity", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "quantity__value", - "annotations": [ - { - "tag": "owl", - "value": "DataProperty, DataHasValue", - "@type": "Annotation" - } - ], - "description": "the value of the quantity", - "from_schema": "https://w3id.org/ontogpt/recipe", - "slot_uri": "http://w3id.org/ontogpt/recipe/value", - "alias": "value", - "owner": "Quantity", - "domain_of": [ - "Quantity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "quantity__unit", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the unit of the quantity, e.g. grams, cups, etc.", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://qudt.org/schema/qudt/unit" - ], - "slot_uri": "http://qudt.org/schema/qudt/unit", - "alias": "unit", - "owner": "Quantity", - "domain_of": [ - "Quantity" - ], - "range": "Unit", - "@type": "SlotDefinition" - }, - { - "name": "step__action", - "description": "the action taken in this step (e.g. mix, add)", - "from_schema": "https://w3id.org/ontogpt/recipe", - "slot_uri": "http://w3id.org/ontogpt/recipe/action", - "alias": "action", - "owner": "Step", - "domain_of": [ - "Step" - ], - "range": "Action", - "@type": "SlotDefinition" - }, - { - "name": "step__inputs", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the inputs of this step", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://purl.obolibrary.org/obo/RO_0002233" - ], - "slot_uri": "http://purl.obolibrary.org/obo/RO_0002233", - "multivalued": true, - "alias": "inputs", - "owner": "Step", - "domain_of": [ - "Step" - ], - "range": "FoodItem", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "step__outputs", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the outputs of this step", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://purl.obolibrary.org/obo/RO_0002234" - ], - "slot_uri": "http://purl.obolibrary.org/obo/RO_0002234", - "multivalued": true, - "alias": "outputs", - "owner": "Step", - "domain_of": [ - "Step" - ], - "range": "FoodItem", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "step__utensils", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the kitchen utensil used in this step (e.g. pan, bowl)", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://purl.obolibrary.org/obo/RO_0002500" - ], - "slot_uri": "http://purl.obolibrary.org/obo/RO_0002500", - "multivalued": true, - "alias": "utensils", - "owner": "Step", - "domain_of": [ - "Step" - ], - "range": "UtensilType", - "@type": "SlotDefinition" - }, - { - "name": "foodItem__food", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the food item", - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "http://purl.obolibrary.org/obo/BFO_0000051" - ], - "slot_uri": "http://purl.obolibrary.org/obo/BFO_0000051", - "alias": "food", - "owner": "FoodItem", - "domain_of": [ - "FoodItem" - ], - "range": "FoodType", - "@type": "SlotDefinition" - }, - { - "name": "foodItem__state", - "annotations": [ - { - "tag": "owl", - "value": "DataProperty, DataHasValue", - "@type": "Annotation" - } - ], - "description": "the state of the food item (e.g. chopped, diced)", - "from_schema": "https://w3id.org/ontogpt/recipe", - "slot_uri": "http://w3id.org/ontogpt/recipe/state", - "alias": "state", - "owner": "FoodItem", - "domain_of": [ - "FoodItem" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Recipe", - "definition_uri": "http://w3id.org/ontogpt/recipe/Recipe", - "annotations": [ - { - "tag": "owl", - "value": "Class", - "@type": "Annotation" - }, - { - "tag": "owl.template", - "value": "EquivalentClasses(\n {{url}}\n ObjectIntersectionOf(\n recipe:Recipe\n \n {% for step in steps %}\n ObjectSomeValuesFrom(\n recipe:steps\n {{tr(step)}}\n )\n {% endfor %}\n {% for ingredient in ingredients %}\n ObjectSomeValuesFrom(\n FOODON:00002420\n {{tr(ingredient)}}\n )\n {% endfor %}\n )\n)\n", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "close_mappings": [ - "FOODON:00004081" - ], - "slots": [ - "recipe__url", - "recipe__label", - "recipe__description", - "recipe__categories", - "recipe__ingredients", - "recipe__steps" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "url", - "annotations": [ - { - "tag": "prompt.ignore", - "value": "True", - "@type": "Annotation" - } - ], - "slot_uri": "rdf:Resource", - "identifier": true, - "range": "uriorcurie", - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "the name of the recipe", - "slot_uri": "rdfs:label", - "@type": "SlotDefinition" - }, - { - "name": "description", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "a brief textual description of the recipe", - "slot_uri": "dcterms:description", - "@type": "SlotDefinition" - }, - { - "name": "categories", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the categories to which this recipe belongs", - "slot_uri": "dcterms:subject", - "multivalued": true, - "range": "RecipeCategory", - "@type": "SlotDefinition" - }, - { - "name": "ingredients", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the ingredients plus quantities of the recipe", - "slot_uri": "FOODON:00002420", - "multivalued": true, - "range": "Ingredient", - "@type": "SlotDefinition" - }, - { - "name": "steps", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the individual steps involved in this recipe", - "multivalued": true, - "range": "Step", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/recipe/Recipe", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Ingredient", - "definition_uri": "http://w3id.org/ontogpt/recipe/Ingredient", - "annotations": [ - { - "tag": "owl", - "value": "IntersectionOf", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "FOODON:00004085" - ], - "is_a": "CompoundExpression", - "slots": [ - "ingredient__food_item", - "ingredient__amount" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "food_item", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the food item", - "range": "FoodItem", - "@type": "SlotDefinition" - }, - { - "name": "amount", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the quantity of the ingredient, e.g. 2 lbs", - "range": "Quantity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://purl.obolibrary.org/obo/FOODON_00004085", - "@type": "ClassDefinition" - }, - { - "name": "Quantity", - "definition_uri": "http://w3id.org/ontogpt/recipe/Quantity", - "annotations": [ - { - "tag": "owl", - "value": "IntersectionOf", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "is_a": "CompoundExpression", - "slots": [ - "quantity__value", - "quantity__unit" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "value", - "annotations": [ - { - "tag": "owl", - "value": "DataProperty, DataHasValue", - "@type": "Annotation" - } - ], - "description": "the value of the quantity", - "@type": "SlotDefinition" - }, - { - "name": "unit", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the unit of the quantity, e.g. grams, cups, etc.", - "slot_uri": "qudt:unit", - "range": "Unit", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/recipe/Quantity", - "@type": "ClassDefinition" - }, - { - "name": "Step", - "definition_uri": "http://w3id.org/ontogpt/recipe/Step", - "annotations": [ - { - "tag": "owl", - "value": "IntersectionOf", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "mappings": [ - "FOODON:00004087" - ], - "is_a": "CompoundExpression", - "slots": [ - "step__action", - "step__inputs", - "step__outputs", - "step__utensils" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "action", - "description": "the action taken in this step (e.g. mix, add)", - "range": "Action", - "@type": "SlotDefinition" - }, - { - "name": "inputs", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the inputs of this step", - "slot_uri": "RO:0002233", - "multivalued": true, - "range": "FoodItem", - "@type": "SlotDefinition" - }, - { - "name": "outputs", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "a semicolon separated list of the outputs of this step", - "slot_uri": "RO:0002234", - "multivalued": true, - "range": "FoodItem", - "@type": "SlotDefinition" - }, - { - "name": "utensils", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the kitchen utensil used in this step (e.g. pan, bowl)", - "slot_uri": "RO:0002500", - "multivalued": true, - "range": "UtensilType", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://purl.obolibrary.org/obo/FOODON_00004087", - "@type": "ClassDefinition" - }, - { - "name": "FoodItem", - "definition_uri": "http://w3id.org/ontogpt/recipe/FoodItem", - "annotations": [ - { - "tag": "owl", - "value": "IntersectionOf", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "is_a": "CompoundExpression", - "slots": [ - "foodItem__food", - "foodItem__state" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "food", - "annotations": [ - { - "tag": "owl", - "value": "ObjectProperty, ObjectSomeValuesFrom", - "@type": "Annotation" - } - ], - "description": "the food item", - "slot_uri": "BFO:0000051", - "range": "FoodType", - "@type": "SlotDefinition" - }, - { - "name": "state", - "annotations": [ - { - "tag": "owl", - "value": "DataProperty, DataHasValue", - "@type": "Annotation" - } - ], - "description": "the state of the food item (e.g. chopped, diced)", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/recipe/FoodItem", - "@type": "ClassDefinition" - }, - { - "name": "FoodType", - "id_prefixes": [ - "dbpediaont", - "FOODON" - ], - "definition_uri": "http://w3id.org/ontogpt/recipe/FoodType", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:foodon, sqlite:obo:dbpediaont", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/recipe/FoodType", - "@type": "ClassDefinition" - }, - { - "name": "RecipeCategory", - "id_prefixes": [ - "dbpediaont", - "FOODON", - "HANCESTRO" - ], - "definition_uri": "http://w3id.org/ontogpt/recipe/RecipeCategory", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:foodon, sqlite:obo:dbpediaont", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/recipe/RecipeCategory", - "@type": "ClassDefinition" - }, - { - "name": "Action", - "id_prefixes": [ - "dbpediaont", - "FOODON" - ], - "definition_uri": "http://w3id.org/ontogpt/recipe/Action", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:dbpediaont, sqlite:obo:foodon", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/recipe/Action", - "@type": "ClassDefinition" - }, - { - "name": "UtensilType", - "id_prefixes": [ - "dbpediaont", - "FOODON" - ], - "definition_uri": "http://w3id.org/ontogpt/recipe/UtensilType", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:dbpediaont, sqlite:obo:foodon", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/recipe/UtensilType", - "@type": "ClassDefinition" - }, - { - "name": "Unit", - "id_prefixes": [ - "UO", - "NCIT", - "dbpediaont" - ], - "definition_uri": "http://w3id.org/ontogpt/recipe/Unit", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:uo, sqlite:obo:dbpediaont, sqlite:obo:foodon", - "@type": "Annotation" - } - ], - "from_schema": "https://w3id.org/ontogpt/recipe", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/recipe/Unit", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "recipe.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 5792, - "generation_date": "2023-08-07T10:56:09", - "@type": "SchemaDefinition", - "@context": [ - "projects/recipe/jsonld/recipe.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/recipe/" - } - ] -} diff --git a/projects/recipe/jsonschema/recipe.schema.json b/projects/recipe/jsonschema/recipe.schema.json deleted file mode 100644 index 6c29c2c57..000000000 --- a/projects/recipe/jsonschema/recipe.schema.json +++ /dev/null @@ -1,397 +0,0 @@ -{ - "$defs": { - "Action": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Action", - "type": "object" - }, - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "FoodItem": { - "additionalProperties": false, - "description": "", - "properties": { - "food": { - "description": "the food item", - "type": "string" - }, - "state": { - "description": "the state of the food item (e.g. chopped, diced)", - "type": "string" - } - }, - "title": "FoodItem", - "type": "object" - }, - "FoodType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "FoodType", - "type": "object" - }, - "Ingredient": { - "additionalProperties": false, - "description": "", - "properties": { - "amount": { - "$ref": "#/$defs/Quantity", - "description": "the quantity of the ingredient, e.g. 2 lbs" - }, - "food_item": { - "$ref": "#/$defs/FoodItem", - "description": "the food item" - } - }, - "title": "Ingredient", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "Quantity": { - "additionalProperties": false, - "description": "", - "properties": { - "unit": { - "description": "the unit of the quantity, e.g. grams, cups, etc.", - "type": "string" - }, - "value": { - "description": "the value of the quantity", - "type": "string" - } - }, - "title": "Quantity", - "type": "object" - }, - "Recipe": { - "additionalProperties": false, - "description": "", - "properties": { - "categories": { - "description": "a semicolon separated list of the categories to which this recipe belongs", - "items": { - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a brief textual description of the recipe", - "type": "string" - }, - "ingredients": { - "description": "a semicolon separated list of the ingredients plus quantities of the recipe", - "items": { - "$ref": "#/$defs/Ingredient" - }, - "type": "array" - }, - "label": { - "description": "the name of the recipe", - "type": "string" - }, - "steps": { - "description": "a semicolon separated list of the individual steps involved in this recipe", - "items": { - "$ref": "#/$defs/Step" - }, - "type": "array" - }, - "url": { - "type": "string" - } - }, - "required": [ - "url" - ], - "title": "Recipe", - "type": "object" - }, - "RecipeCategory": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RecipeCategory", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "Step": { - "additionalProperties": false, - "description": "", - "properties": { - "action": { - "description": "the action taken in this step (e.g. mix, add)", - "type": "string" - }, - "inputs": { - "description": "a semicolon separated list of the inputs of this step", - "items": { - "$ref": "#/$defs/FoodItem" - }, - "type": "array" - }, - "outputs": { - "description": "a semicolon separated list of the outputs of this step", - "items": { - "$ref": "#/$defs/FoodItem" - }, - "type": "array" - }, - "utensils": { - "description": "the kitchen utensil used in this step (e.g. pan, bowl)", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "Step", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Unit": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Unit", - "type": "object" - }, - "UtensilType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "UtensilType", - "type": "object" - } - }, - "$id": "https://w3id.org/ontogpt/recipe", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "categories": { - "description": "a semicolon separated list of the categories to which this recipe belongs", - "items": { - "type": "string" - }, - "type": "array" - }, - "description": { - "description": "a brief textual description of the recipe", - "type": "string" - }, - "ingredients": { - "description": "a semicolon separated list of the ingredients plus quantities of the recipe", - "items": { - "$ref": "#/$defs/Ingredient" - }, - "type": "array" - }, - "label": { - "description": "the name of the recipe", - "type": "string" - }, - "steps": { - "description": "a semicolon separated list of the individual steps involved in this recipe", - "items": { - "$ref": "#/$defs/Step" - }, - "type": "array" - }, - "url": { - "type": "string" - } - }, - "required": [ - "url" - ], - "title": "recipe-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/recipe/owl/recipe.owl.ttl b/projects/recipe/owl/recipe.owl.ttl deleted file mode 100644 index 6e74a6b37..000000000 --- a/projects/recipe/owl/recipe.owl.ttl +++ /dev/null @@ -1,624 +0,0 @@ -@prefix BFO: <http://purl.obolibrary.org/obo/BFO_> . -@prefix FOODON: <http://purl.obolibrary.org/obo/FOODON_> . -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix RO: <http://purl.obolibrary.org/obo/RO_> . -@prefix dcterms: <http://purl.org/dc/terms/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix qudt: <http://qudt.org/schema/qudt/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix recipe: <http://w3id.org/ontogpt/recipe/> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<https://w3id.org/ontogpt/recipe> a owl:Ontology ; - rdfs:label "recipe-template" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - recipe:Recipe ; - linkml:classes "{'Recipe': ClassDefinition(name='Recipe', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/recipe/Recipe', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='Class', extensions={}, annotations={}), 'owl.template': Annotation(tag='owl.template', value='EquivalentClasses(\\n {{url}}\\n ObjectIntersectionOf(\\n recipe:Recipe\\n \\n {% for step in steps %}\\n ObjectSomeValuesFrom(\\n recipe:steps\\n {{tr(step)}}\\n )\\n {% endfor %}\\n {% for ingredient in ingredients %}\\n ObjectSomeValuesFrom(\\n FOODON:00002420\\n {{tr(ingredient)}}\\n )\\n {% endfor %}\\n )\\n)\\n', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['FOODON:00004081'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['recipe__url', 'recipe__label', 'recipe__description', 'recipe__categories', 'recipe__ingredients', 'recipe__steps'], slot_usage={}, attributes={'url': SlotDefinition(name='url', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.ignore': Annotation(tag='prompt.ignore', value='True', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdf:Resource', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='uriorcurie', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='the name of the recipe', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='a brief textual description of the recipe', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='dcterms:description', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'categories': SlotDefinition(name='categories', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationAssertion', extensions={}, annotations={})}, description='a semicolon separated list of the categories to which this recipe belongs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='dcterms:subject', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RecipeCategory', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ingredients': SlotDefinition(name='ingredients', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='a semicolon separated list of the ingredients plus quantities of the recipe', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='FOODON:00002420', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Ingredient', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'steps': SlotDefinition(name='steps', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='a semicolon separated list of the individual steps involved in this recipe', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Step', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='recipe:Recipe', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Ingredient': ClassDefinition(name='Ingredient', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/recipe/Ingredient', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='IntersectionOf', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['FOODON:00004085'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['ingredient__food_item', 'ingredient__amount'], slot_usage={}, attributes={'food_item': SlotDefinition(name='food_item', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the food item', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='FoodItem', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'amount': SlotDefinition(name='amount', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the quantity of the ingredient, e.g. 2 lbs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Quantity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='FOODON:00004085', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Quantity': ClassDefinition(name='Quantity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/recipe/Quantity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='IntersectionOf', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['quantity__value', 'quantity__unit'], slot_usage={}, attributes={'value': SlotDefinition(name='value', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='DataProperty, DataHasValue', extensions={}, annotations={})}, description='the value of the quantity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'unit': SlotDefinition(name='unit', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the unit of the quantity, e.g. grams, cups, etc.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='qudt:unit', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Unit', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='recipe:Quantity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Step': ClassDefinition(name='Step', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/recipe/Step', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='IntersectionOf', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['FOODON:00004087'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['step__action', 'step__inputs', 'step__outputs', 'step__utensils'], slot_usage={}, attributes={'action': SlotDefinition(name='action', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the action taken in this step (e.g. mix, add)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Action', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'inputs': SlotDefinition(name='inputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='a semicolon separated list of the inputs of this step', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='RO:0002233', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='FoodItem', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'outputs': SlotDefinition(name='outputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='a semicolon separated list of the outputs of this step', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='RO:0002234', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='FoodItem', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'utensils': SlotDefinition(name='utensils', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the kitchen utensil used in this step (e.g. pan, bowl)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='RO:0002500', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='UtensilType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='FOODON:00004087', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'FoodItem': ClassDefinition(name='FoodItem', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/recipe/FoodItem', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='IntersectionOf', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['foodItem__food', 'foodItem__state'], slot_usage={}, attributes={'food': SlotDefinition(name='food', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the food item', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='BFO:0000051', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='FoodType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'state': SlotDefinition(name='state', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='DataProperty, DataHasValue', extensions={}, annotations={})}, description='the state of the food item (e.g. chopped, diced)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='recipe:FoodItem', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'FoodType': ClassDefinition(name='FoodType', id_prefixes=['dbpediaont', 'FOODON'], definition_uri='http://w3id.org/ontogpt/recipe/FoodType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:foodon, sqlite:obo:dbpediaont', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='recipe:FoodType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RecipeCategory': ClassDefinition(name='RecipeCategory', id_prefixes=['dbpediaont', 'FOODON', 'HANCESTRO'], definition_uri='http://w3id.org/ontogpt/recipe/RecipeCategory', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:foodon, sqlite:obo:dbpediaont', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='recipe:RecipeCategory', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Action': ClassDefinition(name='Action', id_prefixes=['dbpediaont', 'FOODON'], definition_uri='http://w3id.org/ontogpt/recipe/Action', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:dbpediaont, sqlite:obo:foodon', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='recipe:Action', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'UtensilType': ClassDefinition(name='UtensilType', id_prefixes=['dbpediaont', 'FOODON'], definition_uri='http://w3id.org/ontogpt/recipe/UtensilType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:dbpediaont, sqlite:obo:foodon', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='recipe:UtensilType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Unit': ClassDefinition(name='Unit', id_prefixes=['UO', 'NCIT', 'dbpediaont'], definition_uri='http://w3id.org/ontogpt/recipe/Unit', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:uo, sqlite:obo:dbpediaont, sqlite:obo:foodon', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/ontogpt/recipe', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='recipe:Unit', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "https://w3id.org/ontogpt/recipe" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - recipe:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -recipe:Recipe a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Recipe" ; - recipe:owl "Class" ; - recipe:owl.template """EquivalentClasses( - {{url}} - ObjectIntersectionOf( - recipe:Recipe - - {% for step in steps %} - ObjectSomeValuesFrom( - recipe:steps - {{tr(step)}} - ) - {% endfor %} - {% for ingredient in ingredients %} - ObjectSomeValuesFrom( - FOODON:00002420 - {{tr(ingredient)}} - ) - {% endfor %} - ) -) -""" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom recipe:Ingredient ; - owl:onProperty FOODON:00002420 ], - [ a owl:Restriction ; - owl:allValuesFrom recipe:Step ; - owl:onProperty recipe:steps ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty dcterms:description ], - [ a owl:Restriction ; - owl:allValuesFrom recipe:RecipeCategory ; - owl:onProperty dcterms:subject ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ], - [ a owl:Restriction ; - owl:onClass linkml:Uriorcurie ; - owl:onProperty <http://example.org/UNKNOWN/rdf/Resource> ; - owl:qualifiedCardinality 1 ] ; - skos:closeMatch FOODON:00004081 ; - linkml:attributes "{'url': SlotDefinition(name='url', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.ignore': Annotation(tag='prompt.ignore', value='True', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdf:Resource', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='uriorcurie', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='the name of the recipe', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'description': SlotDefinition(name='description', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='a brief textual description of the recipe', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='dcterms:description', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'categories': SlotDefinition(name='categories', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationAssertion', extensions={}, annotations={})}, description='a semicolon separated list of the categories to which this recipe belongs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='dcterms:subject', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RecipeCategory', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ingredients': SlotDefinition(name='ingredients', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='a semicolon separated list of the ingredients plus quantities of the recipe', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='FOODON:00002420', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Ingredient', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'steps': SlotDefinition(name='steps', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='a semicolon separated list of the individual steps involved in this recipe', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Step', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -recipe:action a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "action" ; - rdfs:range recipe:Action ; - skos:definition "the action taken in this step (e.g. mix, add)" . - -recipe:amount a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "amount" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:Quantity ; - skos:definition "the quantity of the ingredient, e.g. 2 lbs" . - -recipe:food_item a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "food_item" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:FoodItem ; - skos:definition "the food item" . - -recipe:state a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "state" ; - recipe:owl "DataProperty, DataHasValue" ; - rdfs:range linkml:String ; - skos:definition "the state of the food item (e.g. chopped, diced)" . - -recipe:steps a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "steps" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:Step ; - skos:definition "a semicolon separated list of the individual steps involved in this recipe" . - -recipe:value a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "value" ; - recipe:owl "DataProperty, DataHasValue" ; - rdfs:range linkml:String ; - skos:definition "the value of the quantity" . - -<http://example.org/UNKNOWN/rdf/Resource> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "url" ; - recipe:prompt.ignore "True" ; - rdfs:range linkml:Uriorcurie ; - skos:exactMatch <http://example.org/UNKNOWN/rdf/Resource> . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition . - -BFO:0000051 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "food" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:FoodType ; - skos:definition "the food item" ; - skos:exactMatch BFO:0000051 . - -FOODON:00002420 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ingredients" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:Ingredient ; - skos:definition "a semicolon separated list of the ingredients plus quantities of the recipe" ; - skos:exactMatch FOODON:00002420 . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -RO:0002233 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "inputs" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:FoodItem ; - skos:definition "a semicolon separated list of the inputs of this step" ; - skos:exactMatch RO:0002233 . - -RO:0002234 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "outputs" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:FoodItem ; - skos:definition "a semicolon separated list of the outputs of this step" ; - skos:exactMatch RO:0002234 . - -RO:0002500 a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "utensils" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:UtensilType ; - skos:definition "the kitchen utensil used in this step (e.g. pan, bowl)" ; - skos:exactMatch RO:0002500 . - -dcterms:description a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "description" ; - recipe:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:definition "a brief textual description of the recipe" ; - skos:exactMatch dcterms:description . - -dcterms:subject a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "categories" ; - recipe:owl "AnnotationAssertion" ; - rdfs:range recipe:RecipeCategory ; - skos:definition "a semicolon separated list of the categories to which this recipe belongs" ; - skos:exactMatch dcterms:subject . - -qudt:unit a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "unit" ; - recipe:owl "ObjectProperty, ObjectSomeValuesFrom" ; - rdfs:range recipe:Unit ; - skos:definition "the unit of the quantity, e.g. grams, cups, etc." ; - skos:exactMatch qudt:unit . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -recipe:Action a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Action" ; - recipe:annotators "sqlite:obo:dbpediaont, sqlite:obo:foodon" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -recipe:FoodType a owl:Class, - linkml:ClassDefinition ; - rdfs:label "FoodType" ; - recipe:annotators "sqlite:obo:foodon, sqlite:obo:dbpediaont" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -recipe:Ingredient a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Ingredient" ; - recipe:owl "IntersectionOf" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass recipe:Quantity ; - owl:onProperty recipe:amount ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass recipe:FoodItem ; - owl:onProperty recipe:food_item ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:exactMatch FOODON:00004085 ; - linkml:attributes "{'food_item': SlotDefinition(name='food_item', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the food item', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='FoodItem', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'amount': SlotDefinition(name='amount', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the quantity of the ingredient, e.g. 2 lbs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Quantity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -recipe:Quantity a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Quantity" ; - recipe:owl "IntersectionOf" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass recipe:Unit ; - owl:onProperty qudt:unit ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty recipe:value ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'value': SlotDefinition(name='value', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='DataProperty, DataHasValue', extensions={}, annotations={})}, description='the value of the quantity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'unit': SlotDefinition(name='unit', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the unit of the quantity, e.g. grams, cups, etc.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='qudt:unit', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Unit', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -recipe:RecipeCategory a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RecipeCategory" ; - recipe:annotators "sqlite:obo:foodon, sqlite:obo:dbpediaont" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -recipe:Step a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Step" ; - recipe:owl "IntersectionOf" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom recipe:UtensilType ; - owl:onProperty RO:0002500 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass recipe:Action ; - owl:onProperty recipe:action ], - [ a owl:Restriction ; - owl:allValuesFrom recipe:FoodItem ; - owl:onProperty RO:0002233 ], - [ a owl:Restriction ; - owl:allValuesFrom recipe:FoodItem ; - owl:onProperty RO:0002234 ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:exactMatch FOODON:00004087 ; - linkml:attributes "{'action': SlotDefinition(name='action', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the action taken in this step (e.g. mix, add)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Action', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'inputs': SlotDefinition(name='inputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='a semicolon separated list of the inputs of this step', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='RO:0002233', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='FoodItem', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'outputs': SlotDefinition(name='outputs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='a semicolon separated list of the outputs of this step', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='RO:0002234', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='FoodItem', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'utensils': SlotDefinition(name='utensils', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the kitchen utensil used in this step (e.g. pan, bowl)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='RO:0002500', multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='UtensilType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -recipe:Unit a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Unit" ; - recipe:annotators "sqlite:obo:uo, sqlite:obo:dbpediaont, sqlite:obo:foodon" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -recipe:UtensilType a owl:Class, - linkml:ClassDefinition ; - rdfs:label "UtensilType" ; - recipe:annotators "sqlite:obo:dbpediaont, sqlite:obo:foodon" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -recipe:FoodItem a owl:Class, - linkml:ClassDefinition ; - rdfs:label "FoodItem" ; - recipe:owl "IntersectionOf" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass recipe:FoodType ; - owl:onProperty BFO:0000051 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty recipe:state ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'food': SlotDefinition(name='food', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='ObjectProperty, ObjectSomeValuesFrom', extensions={}, annotations={})}, description='the food item', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='BFO:0000051', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='FoodType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'state': SlotDefinition(name='state', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='DataProperty, DataHasValue', extensions={}, annotations={})}, description='the state of the food item (e.g. chopped, diced)', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/recipe/prefixmap/recipe.yaml b/projects/recipe/prefixmap/recipe.yaml deleted file mode 100644 index 81b4e434d..000000000 --- a/projects/recipe/prefixmap/recipe.yaml +++ /dev/null @@ -1,51 +0,0 @@ -{ - "AUTO": "http://example.org/auto/", - "BFO": "http://purl.obolibrary.org/obo/BFO_", - "FOODON": "http://purl.obolibrary.org/obo/FOODON_", - "HANCESTRO": "http://purl.obolibrary.org/obo/HANCESTRO_", - "NCIT": "http://purl.obolibrary.org/obo/NCIT_", - "RO": "http://purl.obolibrary.org/obo/RO_", - "UO": "http://purl.obolibrary.org/obo/UO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "dbpediaont": "http://dbpedia.org/ontology/", - "dcterms": "http://purl.org/dc/terms/", - "linkml": "https://w3id.org/linkml/", - "qudt": "http://qudt.org/schema/qudt/", - "rdf": "http://example.org/UNKNOWN/rdf/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "recipe": "http://w3id.org/ontogpt/recipe/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "Ingredient": { - "@id": "FOODON:00004085" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "Step": { - "@id": "FOODON:00004087" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/recipe/protobuf/recipe.proto b/projects/recipe/protobuf/recipe.proto deleted file mode 100644 index 9238d8178..000000000 --- a/projects/recipe/protobuf/recipe.proto +++ /dev/null @@ -1,91 +0,0 @@ -message Action - { - string id = 0 - string label = 0 - } -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message FoodItem - { - foodType food = 0 - string state = 0 - } -message FoodType - { - string id = 0 - string label = 0 - } -message Ingredient - { - foodItem foodItem = 0 - quantity amount = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message Quantity - { - string value = 0 - unit unit = 0 - } -message Recipe - { - uriorcurie url = 0 - string label = 0 - string description = 0 - repeated recipeCategory categories = 0 - repeated ingredient ingredients = 0 - repeated step steps = 0 - } -message RecipeCategory - { - string id = 0 - string label = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message Step - { - action action = 0 - repeated foodItem inputs = 0 - repeated foodItem outputs = 0 - repeated utensilType utensils = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Unit - { - string id = 0 - string label = 0 - } -message UtensilType - { - string id = 0 - string label = 0 - } diff --git a/projects/recipe/recipe.py b/projects/recipe/recipe.py deleted file mode 100644 index 0e868f756..000000000 --- a/projects/recipe/recipe.py +++ /dev/null @@ -1,687 +0,0 @@ -# Auto generated from recipe.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:56:18 -# Schema: recipe-template -# -# id: https://w3id.org/ontogpt/recipe -# description: A template for food recipes -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String, Uriorcurie -from linkml_runtime.utils.metamodelcore import URIorCURIE - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -AUTO = CurieNamespace('AUTO', 'http://example.org/auto/') -BFO = CurieNamespace('BFO', 'http://purl.obolibrary.org/obo/BFO_') -FOODON = CurieNamespace('FOODON', 'http://purl.obolibrary.org/obo/FOODON_') -HANCESTRO = CurieNamespace('HANCESTRO', 'http://purl.obolibrary.org/obo/HANCESTRO_') -NCIT = CurieNamespace('NCIT', 'http://purl.obolibrary.org/obo/NCIT_') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -UO = CurieNamespace('UO', 'http://purl.obolibrary.org/obo/UO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -DBPEDIAONT = CurieNamespace('dbpediaont', 'http://dbpedia.org/ontology/') -DCTERMS = CurieNamespace('dcterms', 'http://purl.org/dc/terms/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -QUDT = CurieNamespace('qudt', 'http://qudt.org/schema/qudt/') -RDF = CurieNamespace('rdf', 'http://example.org/UNKNOWN/rdf/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -RECIPE = CurieNamespace('recipe', 'http://w3id.org/ontogpt/recipe/') -DEFAULT_ = RECIPE - - -# Types - -# Class references -class RecipeUrl(URIorCURIE): - pass - - -class NamedEntityId(extended_str): - pass - - -class FoodTypeId(NamedEntityId): - pass - - -class RecipeCategoryId(NamedEntityId): - pass - - -class ActionId(NamedEntityId): - pass - - -class UtensilTypeId(NamedEntityId): - pass - - -class UnitId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class Recipe(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = RECIPE.Recipe - class_class_curie: ClassVar[str] = "recipe:Recipe" - class_name: ClassVar[str] = "Recipe" - class_model_uri: ClassVar[URIRef] = RECIPE.Recipe - - url: Union[str, RecipeUrl] = None - label: Optional[str] = None - description: Optional[str] = None - categories: Optional[Union[Union[str, RecipeCategoryId], List[Union[str, RecipeCategoryId]]]] = empty_list() - ingredients: Optional[Union[Union[dict, "Ingredient"], List[Union[dict, "Ingredient"]]]] = empty_list() - steps: Optional[Union[Union[dict, "Step"], List[Union[dict, "Step"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.url): - self.MissingRequiredField("url") - if not isinstance(self.url, RecipeUrl): - self.url = RecipeUrl(self.url) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - if self.description is not None and not isinstance(self.description, str): - self.description = str(self.description) - - if not isinstance(self.categories, list): - self.categories = [self.categories] if self.categories is not None else [] - self.categories = [v if isinstance(v, RecipeCategoryId) else RecipeCategoryId(v) for v in self.categories] - - if not isinstance(self.ingredients, list): - self.ingredients = [self.ingredients] if self.ingredients is not None else [] - self.ingredients = [v if isinstance(v, Ingredient) else Ingredient(**as_dict(v)) for v in self.ingredients] - - if not isinstance(self.steps, list): - self.steps = [self.steps] if self.steps is not None else [] - self.steps = [v if isinstance(v, Step) else Step(**as_dict(v)) for v in self.steps] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = RECIPE.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = RECIPE.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class FoodType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = RECIPE.FoodType - class_class_curie: ClassVar[str] = "recipe:FoodType" - class_name: ClassVar[str] = "FoodType" - class_model_uri: ClassVar[URIRef] = RECIPE.FoodType - - id: Union[str, FoodTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, FoodTypeId): - self.id = FoodTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class RecipeCategory(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = RECIPE.RecipeCategory - class_class_curie: ClassVar[str] = "recipe:RecipeCategory" - class_name: ClassVar[str] = "RecipeCategory" - class_model_uri: ClassVar[URIRef] = RECIPE.RecipeCategory - - id: Union[str, RecipeCategoryId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RecipeCategoryId): - self.id = RecipeCategoryId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Action(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = RECIPE.Action - class_class_curie: ClassVar[str] = "recipe:Action" - class_name: ClassVar[str] = "Action" - class_model_uri: ClassVar[URIRef] = RECIPE.Action - - id: Union[str, ActionId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, ActionId): - self.id = ActionId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class UtensilType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = RECIPE.UtensilType - class_class_curie: ClassVar[str] = "recipe:UtensilType" - class_name: ClassVar[str] = "UtensilType" - class_model_uri: ClassVar[URIRef] = RECIPE.UtensilType - - id: Union[str, UtensilTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, UtensilTypeId): - self.id = UtensilTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Unit(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = RECIPE.Unit - class_class_curie: ClassVar[str] = "recipe:Unit" - class_name: ClassVar[str] = "Unit" - class_model_uri: ClassVar[URIRef] = RECIPE.Unit - - id: Union[str, UnitId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, UnitId): - self.id = UnitId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = RECIPE.CompoundExpression - - -@dataclass -class Ingredient(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = FOODON["00004085"] - class_class_curie: ClassVar[str] = "FOODON:00004085" - class_name: ClassVar[str] = "Ingredient" - class_model_uri: ClassVar[URIRef] = RECIPE.Ingredient - - food_item: Optional[Union[dict, "FoodItem"]] = None - amount: Optional[Union[dict, "Quantity"]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.food_item is not None and not isinstance(self.food_item, FoodItem): - self.food_item = FoodItem(**as_dict(self.food_item)) - - if self.amount is not None and not isinstance(self.amount, Quantity): - self.amount = Quantity(**as_dict(self.amount)) - - super().__post_init__(**kwargs) - - -@dataclass -class Quantity(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = RECIPE.Quantity - class_class_curie: ClassVar[str] = "recipe:Quantity" - class_name: ClassVar[str] = "Quantity" - class_model_uri: ClassVar[URIRef] = RECIPE.Quantity - - value: Optional[str] = None - unit: Optional[Union[str, UnitId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.value is not None and not isinstance(self.value, str): - self.value = str(self.value) - - if self.unit is not None and not isinstance(self.unit, UnitId): - self.unit = UnitId(self.unit) - - super().__post_init__(**kwargs) - - -@dataclass -class Step(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = FOODON["00004087"] - class_class_curie: ClassVar[str] = "FOODON:00004087" - class_name: ClassVar[str] = "Step" - class_model_uri: ClassVar[URIRef] = RECIPE.Step - - action: Optional[Union[str, ActionId]] = None - inputs: Optional[Union[Union[dict, "FoodItem"], List[Union[dict, "FoodItem"]]]] = empty_list() - outputs: Optional[Union[Union[dict, "FoodItem"], List[Union[dict, "FoodItem"]]]] = empty_list() - utensils: Optional[Union[Union[str, UtensilTypeId], List[Union[str, UtensilTypeId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.action is not None and not isinstance(self.action, ActionId): - self.action = ActionId(self.action) - - if not isinstance(self.inputs, list): - self.inputs = [self.inputs] if self.inputs is not None else [] - self.inputs = [v if isinstance(v, FoodItem) else FoodItem(**as_dict(v)) for v in self.inputs] - - if not isinstance(self.outputs, list): - self.outputs = [self.outputs] if self.outputs is not None else [] - self.outputs = [v if isinstance(v, FoodItem) else FoodItem(**as_dict(v)) for v in self.outputs] - - if not isinstance(self.utensils, list): - self.utensils = [self.utensils] if self.utensils is not None else [] - self.utensils = [v if isinstance(v, UtensilTypeId) else UtensilTypeId(v) for v in self.utensils] - - super().__post_init__(**kwargs) - - -@dataclass -class FoodItem(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = RECIPE.FoodItem - class_class_curie: ClassVar[str] = "recipe:FoodItem" - class_name: ClassVar[str] = "FoodItem" - class_model_uri: ClassVar[URIRef] = RECIPE.FoodItem - - food: Optional[Union[str, FoodTypeId]] = None - state: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.food is not None and not isinstance(self.food, FoodTypeId): - self.food = FoodTypeId(self.food) - - if self.state is not None and not isinstance(self.state, str): - self.state = str(self.state) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = RECIPE.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = RECIPE.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = RECIPE.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = RECIPE.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = RECIPE.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.recipe__url = Slot(uri=RDF.Resource, name="recipe__url", curie=RDF.curie('Resource'), - model_uri=RECIPE.recipe__url, domain=None, range=URIRef) - -slots.recipe__label = Slot(uri=RDFS.label, name="recipe__label", curie=RDFS.curie('label'), - model_uri=RECIPE.recipe__label, domain=None, range=Optional[str]) - -slots.recipe__description = Slot(uri=DCTERMS.description, name="recipe__description", curie=DCTERMS.curie('description'), - model_uri=RECIPE.recipe__description, domain=None, range=Optional[str]) - -slots.recipe__categories = Slot(uri=DCTERMS.subject, name="recipe__categories", curie=DCTERMS.curie('subject'), - model_uri=RECIPE.recipe__categories, domain=None, range=Optional[Union[Union[str, RecipeCategoryId], List[Union[str, RecipeCategoryId]]]]) - -slots.recipe__ingredients = Slot(uri=FOODON['00002420'], name="recipe__ingredients", curie=FOODON.curie('00002420'), - model_uri=RECIPE.recipe__ingredients, domain=None, range=Optional[Union[Union[dict, Ingredient], List[Union[dict, Ingredient]]]]) - -slots.recipe__steps = Slot(uri=RECIPE.steps, name="recipe__steps", curie=RECIPE.curie('steps'), - model_uri=RECIPE.recipe__steps, domain=None, range=Optional[Union[Union[dict, Step], List[Union[dict, Step]]]]) - -slots.ingredient__food_item = Slot(uri=RECIPE.food_item, name="ingredient__food_item", curie=RECIPE.curie('food_item'), - model_uri=RECIPE.ingredient__food_item, domain=None, range=Optional[Union[dict, FoodItem]]) - -slots.ingredient__amount = Slot(uri=RECIPE.amount, name="ingredient__amount", curie=RECIPE.curie('amount'), - model_uri=RECIPE.ingredient__amount, domain=None, range=Optional[Union[dict, Quantity]]) - -slots.quantity__value = Slot(uri=RECIPE.value, name="quantity__value", curie=RECIPE.curie('value'), - model_uri=RECIPE.quantity__value, domain=None, range=Optional[str]) - -slots.quantity__unit = Slot(uri=QUDT.unit, name="quantity__unit", curie=QUDT.curie('unit'), - model_uri=RECIPE.quantity__unit, domain=None, range=Optional[Union[str, UnitId]]) - -slots.step__action = Slot(uri=RECIPE.action, name="step__action", curie=RECIPE.curie('action'), - model_uri=RECIPE.step__action, domain=None, range=Optional[Union[str, ActionId]]) - -slots.step__inputs = Slot(uri=RO['0002233'], name="step__inputs", curie=RO.curie('0002233'), - model_uri=RECIPE.step__inputs, domain=None, range=Optional[Union[Union[dict, FoodItem], List[Union[dict, FoodItem]]]]) - -slots.step__outputs = Slot(uri=RO['0002234'], name="step__outputs", curie=RO.curie('0002234'), - model_uri=RECIPE.step__outputs, domain=None, range=Optional[Union[Union[dict, FoodItem], List[Union[dict, FoodItem]]]]) - -slots.step__utensils = Slot(uri=RO['0002500'], name="step__utensils", curie=RO.curie('0002500'), - model_uri=RECIPE.step__utensils, domain=None, range=Optional[Union[Union[str, UtensilTypeId], List[Union[str, UtensilTypeId]]]]) - -slots.foodItem__food = Slot(uri=BFO['0000051'], name="foodItem__food", curie=BFO.curie('0000051'), - model_uri=RECIPE.foodItem__food, domain=None, range=Optional[Union[str, FoodTypeId]]) - -slots.foodItem__state = Slot(uri=RECIPE.state, name="foodItem__state", curie=RECIPE.curie('state'), - model_uri=RECIPE.foodItem__state, domain=None, range=Optional[str]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=RECIPE.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=RECIPE.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=RECIPE.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=RECIPE.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=RECIPE.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=RECIPE.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=RECIPE.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=RECIPE.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=RECIPE.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=RECIPE.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=RECIPE.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=RECIPE.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=RECIPE.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=RECIPE.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=RECIPE.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=RECIPE.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=RECIPE.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=RECIPE.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=RECIPE.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=RECIPE.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=RECIPE.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=RECIPE.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=RECIPE.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=RECIPE.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=RECIPE.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/recipe/shacl/recipe.shacl.ttl b/projects/recipe/shacl/recipe.shacl.ttl deleted file mode 100644 index bdf47cb6d..000000000 --- a/projects/recipe/shacl/recipe.shacl.ttl +++ /dev/null @@ -1,343 +0,0 @@ -@prefix BFO: <http://purl.obolibrary.org/obo/BFO_> . -@prefix FOODON: <http://purl.obolibrary.org/obo/FOODON_> . -@prefix RO: <http://purl.obolibrary.org/obo/RO_> . -@prefix dcterms: <http://purl.org/dc/terms/> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix qudt: <http://qudt.org/schema/qudt/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix recipe: <http://w3id.org/ontogpt/recipe/> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -recipe:Recipe a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "the name of the recipe" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:class recipe:RecipeCategory ; - sh:description "a semicolon separated list of the categories to which this recipe belongs" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path dcterms:subject ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <rdf:Resource> ], - [ sh:class FOODON:00004085 ; - sh:description "a semicolon separated list of the ingredients plus quantities of the recipe" ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path FOODON:00002420 ], - [ sh:class FOODON:00004087 ; - sh:description "a semicolon separated list of the individual steps involved in this recipe" ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path recipe:steps ], - [ sh:description "a brief textual description of the recipe" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path dcterms:description ] ; - sh:targetClass recipe:Recipe . - -FOODON:00004085 a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class recipe:FoodItem ; - sh:description "the food item" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path recipe:food_item ], - [ sh:class recipe:Quantity ; - sh:description "the quantity of the ingredient, e.g. 2 lbs" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path recipe:amount ] ; - sh:targetClass FOODON:00004085 . - -FOODON:00004087 a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class recipe:Action ; - sh:description "the action taken in this step (e.g. mix, add)" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path recipe:action ], - [ sh:class recipe:FoodItem ; - sh:description "a semicolon separated list of the inputs of this step" ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path RO:0002233 ], - [ sh:class recipe:UtensilType ; - sh:description "the kitchen utensil used in this step (e.g. pan, bowl)" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path RO:0002500 ], - [ sh:class recipe:FoodItem ; - sh:description "a semicolon separated list of the outputs of this step" ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path RO:0002234 ] ; - sh:targetClass FOODON:00004087 . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -recipe:Action a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass recipe:Action . - -recipe:FoodType a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass recipe:FoodType . - -recipe:Quantity a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class recipe:Unit ; - sh:description "the unit of the quantity, e.g. grams, cups, etc." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path qudt:unit ], - [ sh:description "the value of the quantity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path recipe:value ] ; - sh:targetClass recipe:Quantity . - -recipe:RecipeCategory a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass recipe:RecipeCategory . - -recipe:Unit a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass recipe:Unit . - -recipe:UtensilType a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass recipe:UtensilType . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -recipe:FoodItem a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class recipe:FoodType ; - sh:description "the food item" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path BFO:0000051 ], - [ sh:description "the state of the food item (e.g. chopped, diced)" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path recipe:state ] ; - sh:targetClass recipe:FoodItem . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - diff --git a/projects/recipe/shex/recipe.shex b/projects/recipe/shex/recipe.shex deleted file mode 100644 index 1eedc7b1c..000000000 --- a/projects/recipe/shex/recipe.shex +++ /dev/null @@ -1,231 +0,0 @@ -BASE <http://w3id.org/ontogpt/recipe/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX dcterms: <http://purl.org/dc/terms/> -PREFIX qudt: <http://qudt.org/schema/qudt/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -<Action> CLOSED { - ( $<Action_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Action> ] - ) -} - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - @<FoodItem> OR @<Ingredient> OR @<Quantity> OR @<Step> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<FoodItem> CLOSED { - ( $<FoodItem_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <http://purl.obolibrary.org/obo/BFO_0000051> @<FoodType> ? ; - <state> @linkml:String ? - ) ; - rdf:type [ <FoodItem> ] ? - ) -} - -<FoodType> CLOSED { - ( $<FoodType_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <FoodType> ] - ) -} - -<Ingredient> CLOSED { - ( $<Ingredient_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <food_item> @<FoodItem> ? ; - <amount> @<Quantity> ? - ) ; - rdf:type [ <http://purl.obolibrary.org/obo/FOODON_00004085> ] ? - ) -} - -core:NamedEntity ( - @<Action> OR @<FoodType> OR @<RecipeCategory> OR @core:RelationshipType OR @<Unit> OR @<UtensilType> -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -<Quantity> CLOSED { - ( $<Quantity_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <value> @linkml:String ? ; - qudt:unit @<Unit> ? - ) ; - rdf:type [ <Quantity> ] ? - ) -} - -<Recipe> CLOSED { - ( $<Recipe_tes> ( rdfs1:label @linkml:String ? ; - dcterms:description @linkml:String ? ; - dcterms:subject @<RecipeCategory> * ; - <http://purl.obolibrary.org/obo/FOODON_00002420> @<Ingredient> * ; - <steps> @<Step> * - ) ; - rdf:type [ <Recipe> ] - ) -} - -<RecipeCategory> CLOSED { - ( $<RecipeCategory_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <RecipeCategory> ] - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -<Step> CLOSED { - ( $<Step_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <action> @<Action> ? ; - <http://purl.obolibrary.org/obo/RO_0002233> @<FoodItem> * ; - <http://purl.obolibrary.org/obo/RO_0002234> @<FoodItem> * ; - <http://purl.obolibrary.org/obo/RO_0002500> @<UtensilType> * - ) ; - rdf:type [ <http://purl.obolibrary.org/obo/FOODON_00004087> ] ? - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - -<Unit> CLOSED { - ( $<Unit_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Unit> ] - ) -} - -<UtensilType> CLOSED { - ( $<UtensilType_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <UtensilType> ] - ) -} - - diff --git a/projects/recipe/sqlschema/recipe.sql b/projects/recipe/sqlschema/recipe.sql deleted file mode 100644 index 0219330df..000000000 --- a/projects/recipe/sqlschema/recipe.sql +++ /dev/null @@ -1,112 +0,0 @@ - - -CREATE TABLE "Action" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "FoodType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "Recipe" ( - url TEXT NOT NULL, - label TEXT, - description TEXT, - PRIMARY KEY (url) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Unit" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "UtensilType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "FoodItem" ( - food TEXT, - state TEXT, - PRIMARY KEY (food, state), - FOREIGN KEY(food) REFERENCES "FoodType" (id) -); - -CREATE TABLE "Ingredient" ( - food_item TEXT, - amount TEXT, - "Recipe_url" TEXT, - PRIMARY KEY (food_item, amount, "Recipe_url"), - FOREIGN KEY("Recipe_url") REFERENCES "Recipe" (url) -); - -CREATE TABLE "Quantity" ( - value TEXT, - unit TEXT, - PRIMARY KEY (value, unit), - FOREIGN KEY(unit) REFERENCES "Unit" (id) -); - -CREATE TABLE "RecipeCategory" ( - id TEXT NOT NULL, - label TEXT, - "Recipe_url" TEXT, - PRIMARY KEY (id), - FOREIGN KEY("Recipe_url") REFERENCES "Recipe" (url) -); - -CREATE TABLE "Step" ( - action TEXT, - inputs TEXT, - outputs TEXT, - utensils TEXT, - "Recipe_url" TEXT, - PRIMARY KEY (action, inputs, outputs, utensils, "Recipe_url"), - FOREIGN KEY(action) REFERENCES "Action" (id), - FOREIGN KEY("Recipe_url") REFERENCES "Recipe" (url) -); diff --git a/projects/traits/docs/AnnotatorResult.md b/projects/traits/docs/AnnotatorResult.md deleted file mode 100644 index e10c9d367..000000000 --- a/projects/traits/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [traits:AnnotatorResult](http://w3id.org/ontogpt/traits/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/traits/docs/Any.md b/projects/traits/docs/Any.md deleted file mode 100644 index 4a2c73eee..000000000 --- a/projects/traits/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [traits:Any](http://w3id.org/ontogpt/traits/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/traits/docs/CompoundExpression.md b/projects/traits/docs/CompoundExpression.md deleted file mode 100644 index bb651e01c..000000000 --- a/projects/traits/docs/CompoundExpression.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [traits:CompoundExpression](http://w3id.org/ontogpt/traits/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[CompoundExpression]^-[Triple]) - -## Children - - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/traits/docs/ExtractionResult.md b/projects/traits/docs/ExtractionResult.md deleted file mode 100644 index 317422990..000000000 --- a/projects/traits/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [traits:ExtractionResult](http://w3id.org/ontogpt/traits/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/traits/docs/NamedEntity.md b/projects/traits/docs/NamedEntity.md deleted file mode 100644 index 15f13f911..000000000 --- a/projects/traits/docs/NamedEntity.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [traits:NamedEntity](http://w3id.org/ontogpt/traits/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Trait],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Trait],[NamedEntity]^-[RelationshipType],[Triple])](https://yuml.me/diagram/nofunky;dir:TB/class/[Trait],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Trait],[NamedEntity]^-[RelationshipType],[Triple]) - -## Children - - * [RelationshipType](RelationshipType.md) - * [Trait](Trait.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/traits/docs/NullDataOptions.md b/projects/traits/docs/NullDataOptions.md deleted file mode 100644 index cb9a038f3..000000000 --- a/projects/traits/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [traits:NullDataOptions](http://w3id.org/ontogpt/traits/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/traits/docs/Publication.md b/projects/traits/docs/Publication.md deleted file mode 100644 index 7299f4469..000000000 --- a/projects/traits/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [traits:Publication](http://w3id.org/ontogpt/traits/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/traits/docs/RelationshipType.md b/projects/traits/docs/RelationshipType.md deleted file mode 100644 index 22477ca9b..000000000 --- a/projects/traits/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [traits:RelationshipType](http://w3id.org/ontogpt/traits/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/traits/docs/Taxon.md b/projects/traits/docs/Taxon.md deleted file mode 100644 index 682670fd6..000000000 --- a/projects/traits/docs/Taxon.md +++ /dev/null @@ -1,43 +0,0 @@ - -# Class: Taxon - - - - -URI: [traits:Taxon](http://w3id.org/ontogpt/traits/Taxon) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Trait],[Trait]<preferred_environments%200..*-%20[Taxon],[Trait]<phenotypic_plasticiticy_traits%200..*-%20[Taxon],[Trait]<survival_traits%200..*-%20[Taxon],[Trait]<reproductive_traits%200..*-%20[Taxon],[Trait]<ecological_traits%200..*-%20[Taxon],[Trait]<cellular_traits%200..*-%20[Taxon],[Trait]<genetic_traits%200..*-%20[Taxon],[Trait]<morphological_traits%200..*-%20[Taxon],[Trait]<metabolic_traits%200..*-%20[Taxon])](https://yuml.me/diagram/nofunky;dir:TB/class/[Trait],[Trait]<preferred_environments%200..*-%20[Taxon],[Trait]<phenotypic_plasticiticy_traits%200..*-%20[Taxon],[Trait]<survival_traits%200..*-%20[Taxon],[Trait]<reproductive_traits%200..*-%20[Taxon],[Trait]<ecological_traits%200..*-%20[Taxon],[Trait]<cellular_traits%200..*-%20[Taxon],[Trait]<genetic_traits%200..*-%20[Taxon],[Trait]<morphological_traits%200..*-%20[Taxon],[Trait]<metabolic_traits%200..*-%20[Taxon]) - -## Attributes - - -### Own - - * [➞metabolic_traits](taxon__metabolic_traits.md) <sub>0..\*</sub> - * Description: The metabolic traits for the taxon. - * Range: [Trait](Trait.md) - * [➞morphological_traits](taxon__morphological_traits.md) <sub>0..\*</sub> - * Description: The morphological traits for the taxon. - * Range: [Trait](Trait.md) - * [➞genetic_traits](taxon__genetic_traits.md) <sub>0..\*</sub> - * Description: The genetic traits for the taxon. - * Range: [Trait](Trait.md) - * [➞cellular_traits](taxon__cellular_traits.md) <sub>0..\*</sub> - * Description: The cellular traits for the taxon. - * Range: [Trait](Trait.md) - * [➞ecological_traits](taxon__ecological_traits.md) <sub>0..\*</sub> - * Description: The ecological traits for the taxon. - * Range: [Trait](Trait.md) - * [➞reproductive_traits](taxon__reproductive_traits.md) <sub>0..\*</sub> - * Description: The reproductive traits for the taxon. - * Range: [Trait](Trait.md) - * [➞survival_traits](taxon__survival_traits.md) <sub>0..\*</sub> - * Description: The survival traits for the taxon. - * Range: [Trait](Trait.md) - * [➞phenotypic_plasticiticy_traits](taxon__phenotypic_plasticiticy_traits.md) <sub>0..\*</sub> - * Description: The phenotypic plasticiticy traits for the taxon. - * Range: [Trait](Trait.md) - * [➞preferred_environments](taxon__preferred_environments.md) <sub>0..\*</sub> - * Description: The preferred environments for the taxon. - * Range: [Trait](Trait.md) diff --git a/projects/traits/docs/TextWithTriples.md b/projects/traits/docs/TextWithTriples.md deleted file mode 100644 index f8b5b4fce..000000000 --- a/projects/traits/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [traits:TextWithTriples](http://w3id.org/ontogpt/traits/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/traits/docs/Trait.md b/projects/traits/docs/Trait.md deleted file mode 100644 index cc2473fff..000000000 --- a/projects/traits/docs/Trait.md +++ /dev/null @@ -1,46 +0,0 @@ - -# Class: Trait - - - - -URI: [traits:Trait](http://w3id.org/ontogpt/traits/Trait) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Taxon]-%20cellular_traits%200..*>[Trait|id(i):string;label(i):string%20%3F],[Taxon]-%20ecological_traits%200..*>[Trait],[Taxon]-%20genetic_traits%200..*>[Trait],[Taxon]-%20metabolic_traits%200..*>[Trait],[Taxon]-%20morphological_traits%200..*>[Trait],[Taxon]-%20phenotypic_plasticiticy_traits%200..*>[Trait],[Taxon]-%20preferred_environments%200..*>[Trait],[Taxon]-%20reproductive_traits%200..*>[Trait],[Taxon]-%20survival_traits%200..*>[Trait],[NamedEntity]^-[Trait],[Taxon],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Taxon]-%20cellular_traits%200..*>[Trait|id(i):string;label(i):string%20%3F],[Taxon]-%20ecological_traits%200..*>[Trait],[Taxon]-%20genetic_traits%200..*>[Trait],[Taxon]-%20metabolic_traits%200..*>[Trait],[Taxon]-%20morphological_traits%200..*>[Trait],[Taxon]-%20phenotypic_plasticiticy_traits%200..*>[Trait],[Taxon]-%20preferred_environments%200..*>[Trait],[Taxon]-%20reproductive_traits%200..*>[Trait],[Taxon]-%20survival_traits%200..*>[Trait],[NamedEntity]^-[Trait],[Taxon],[NamedEntity]) - -## Identifier prefixes - - * ECOCORE - * PATO - * GO - * OBA - * BIODIVTHES - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞cellular_traits](taxon__cellular_traits.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - * **None** *[➞ecological_traits](taxon__ecological_traits.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - * **None** *[➞genetic_traits](taxon__genetic_traits.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - * **None** *[➞metabolic_traits](taxon__metabolic_traits.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - * **None** *[➞morphological_traits](taxon__morphological_traits.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - * **None** *[➞phenotypic_plasticiticy_traits](taxon__phenotypic_plasticiticy_traits.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - * **None** *[➞preferred_environments](taxon__preferred_environments.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - * **None** *[➞reproductive_traits](taxon__reproductive_traits.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - * **None** *[➞survival_traits](taxon__survival_traits.md)* <sub>0..\*</sub> **[Trait](Trait.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/traits/docs/Triple.md b/projects/traits/docs/Triple.md deleted file mode 100644 index ebd00345c..000000000 --- a/projects/traits/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [traits:Triple](http://w3id.org/ontogpt/traits/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/traits/docs/annotatorResult__object_id.md b/projects/traits/docs/annotatorResult__object_id.md deleted file mode 100644 index b026238c9..000000000 --- a/projects/traits/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [traits:annotatorResult__object_id](http://w3id.org/ontogpt/traits/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/traits/docs/annotatorResult__object_text.md b/projects/traits/docs/annotatorResult__object_text.md deleted file mode 100644 index 4c878a3ca..000000000 --- a/projects/traits/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [traits:annotatorResult__object_text](http://w3id.org/ontogpt/traits/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/traits/docs/annotatorResult__subject_text.md b/projects/traits/docs/annotatorResult__subject_text.md deleted file mode 100644 index 36c413e76..000000000 --- a/projects/traits/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [traits:annotatorResult__subject_text](http://w3id.org/ontogpt/traits/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/traits/docs/extractionResult__extracted_object.md b/projects/traits/docs/extractionResult__extracted_object.md deleted file mode 100644 index af596bbf2..000000000 --- a/projects/traits/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [traits:extractionResult__extracted_object](http://w3id.org/ontogpt/traits/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/traits/docs/extractionResult__input_id.md b/projects/traits/docs/extractionResult__input_id.md deleted file mode 100644 index 5841eb865..000000000 --- a/projects/traits/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [traits:extractionResult__input_id](http://w3id.org/ontogpt/traits/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/traits/docs/extractionResult__input_text.md b/projects/traits/docs/extractionResult__input_text.md deleted file mode 100644 index 0882e1796..000000000 --- a/projects/traits/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [traits:extractionResult__input_text](http://w3id.org/ontogpt/traits/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/traits/docs/extractionResult__input_title.md b/projects/traits/docs/extractionResult__input_title.md deleted file mode 100644 index d0c6251eb..000000000 --- a/projects/traits/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [traits:extractionResult__input_title](http://w3id.org/ontogpt/traits/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/traits/docs/extractionResult__named_entities.md b/projects/traits/docs/extractionResult__named_entities.md deleted file mode 100644 index fdd763859..000000000 --- a/projects/traits/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [traits:extractionResult__named_entities](http://w3id.org/ontogpt/traits/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/traits/docs/extractionResult__prompt.md b/projects/traits/docs/extractionResult__prompt.md deleted file mode 100644 index f637fbce5..000000000 --- a/projects/traits/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [traits:extractionResult__prompt](http://w3id.org/ontogpt/traits/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/traits/docs/extractionResult__raw_completion_output.md b/projects/traits/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 15bfec7a7..000000000 --- a/projects/traits/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [traits:extractionResult__raw_completion_output](http://w3id.org/ontogpt/traits/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/traits/docs/namedEntity__id.md b/projects/traits/docs/namedEntity__id.md deleted file mode 100644 index 1c92fed5a..000000000 --- a/projects/traits/docs/namedEntity__id.md +++ /dev/null @@ -1,31 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [traits:namedEntity__id](http://w3id.org/ontogpt/traits/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Trait](Trait.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/traits/docs/namedEntity__label.md b/projects/traits/docs/namedEntity__label.md deleted file mode 100644 index 47b15a216..000000000 --- a/projects/traits/docs/namedEntity__label.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [traits:namedEntity__label](http://w3id.org/ontogpt/traits/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Trait](Trait.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/traits/docs/publication__abstract.md b/projects/traits/docs/publication__abstract.md deleted file mode 100644 index f54714106..000000000 --- a/projects/traits/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [traits:publication__abstract](http://w3id.org/ontogpt/traits/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/traits/docs/publication__combined_text.md b/projects/traits/docs/publication__combined_text.md deleted file mode 100644 index ce6d7aad4..000000000 --- a/projects/traits/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [traits:publication__combined_text](http://w3id.org/ontogpt/traits/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/traits/docs/publication__full_text.md b/projects/traits/docs/publication__full_text.md deleted file mode 100644 index 54692c4f5..000000000 --- a/projects/traits/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [traits:publication__full_text](http://w3id.org/ontogpt/traits/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/traits/docs/publication__id.md b/projects/traits/docs/publication__id.md deleted file mode 100644 index 9676d3df5..000000000 --- a/projects/traits/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [traits:publication__id](http://w3id.org/ontogpt/traits/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/traits/docs/publication__title.md b/projects/traits/docs/publication__title.md deleted file mode 100644 index 194d3364e..000000000 --- a/projects/traits/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [traits:publication__title](http://w3id.org/ontogpt/traits/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/traits/docs/taxon__cellular_traits.md b/projects/traits/docs/taxon__cellular_traits.md deleted file mode 100644 index ef120a5ba..000000000 --- a/projects/traits/docs/taxon__cellular_traits.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: cellular_traits - - -The cellular traits for the taxon. - -URI: [traits:taxon__cellular_traits](http://w3id.org/ontogpt/traits/taxon__cellular_traits) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/taxon__ecological_traits.md b/projects/traits/docs/taxon__ecological_traits.md deleted file mode 100644 index 309b64561..000000000 --- a/projects/traits/docs/taxon__ecological_traits.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: ecological_traits - - -The ecological traits for the taxon. - -URI: [traits:taxon__ecological_traits](http://w3id.org/ontogpt/traits/taxon__ecological_traits) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/taxon__genetic_traits.md b/projects/traits/docs/taxon__genetic_traits.md deleted file mode 100644 index b4de8e391..000000000 --- a/projects/traits/docs/taxon__genetic_traits.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: genetic_traits - - -The genetic traits for the taxon. - -URI: [traits:taxon__genetic_traits](http://w3id.org/ontogpt/traits/taxon__genetic_traits) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/taxon__metabolic_traits.md b/projects/traits/docs/taxon__metabolic_traits.md deleted file mode 100644 index dd3430938..000000000 --- a/projects/traits/docs/taxon__metabolic_traits.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: metabolic_traits - - -The metabolic traits for the taxon. - -URI: [traits:taxon__metabolic_traits](http://w3id.org/ontogpt/traits/taxon__metabolic_traits) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/taxon__morphological_traits.md b/projects/traits/docs/taxon__morphological_traits.md deleted file mode 100644 index 0da5f0d30..000000000 --- a/projects/traits/docs/taxon__morphological_traits.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: morphological_traits - - -The morphological traits for the taxon. - -URI: [traits:taxon__morphological_traits](http://w3id.org/ontogpt/traits/taxon__morphological_traits) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/taxon__phenotypic_plasticiticy_traits.md b/projects/traits/docs/taxon__phenotypic_plasticiticy_traits.md deleted file mode 100644 index 25ef50a48..000000000 --- a/projects/traits/docs/taxon__phenotypic_plasticiticy_traits.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: phenotypic_plasticiticy_traits - - -The phenotypic plasticiticy traits for the taxon. - -URI: [traits:taxon__phenotypic_plasticiticy_traits](http://w3id.org/ontogpt/traits/taxon__phenotypic_plasticiticy_traits) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/taxon__preferred_environments.md b/projects/traits/docs/taxon__preferred_environments.md deleted file mode 100644 index 6f84ea5fb..000000000 --- a/projects/traits/docs/taxon__preferred_environments.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: preferred_environments - - -The preferred environments for the taxon. - -URI: [traits:taxon__preferred_environments](http://w3id.org/ontogpt/traits/taxon__preferred_environments) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/taxon__reproductive_traits.md b/projects/traits/docs/taxon__reproductive_traits.md deleted file mode 100644 index 6cb428c57..000000000 --- a/projects/traits/docs/taxon__reproductive_traits.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: reproductive_traits - - -The reproductive traits for the taxon. - -URI: [traits:taxon__reproductive_traits](http://w3id.org/ontogpt/traits/taxon__reproductive_traits) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/taxon__survival_traits.md b/projects/traits/docs/taxon__survival_traits.md deleted file mode 100644 index 6e69f9634..000000000 --- a/projects/traits/docs/taxon__survival_traits.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: survival_traits - - -The survival traits for the taxon. - -URI: [traits:taxon__survival_traits](http://w3id.org/ontogpt/traits/taxon__survival_traits) - - -## Domain and Range - -None → <sub>0..\*</sub> [Trait](Trait.md) - -## Parents - - -## Children - - -## Used by - - * [Taxon](Taxon.md) diff --git a/projects/traits/docs/textWithTriples__publication.md b/projects/traits/docs/textWithTriples__publication.md deleted file mode 100644 index adc637c95..000000000 --- a/projects/traits/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [traits:textWithTriples__publication](http://w3id.org/ontogpt/traits/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/traits/docs/textWithTriples__triples.md b/projects/traits/docs/textWithTriples__triples.md deleted file mode 100644 index 5fe3ee468..000000000 --- a/projects/traits/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [traits:textWithTriples__triples](http://w3id.org/ontogpt/traits/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/traits/docs/traits.md b/projects/traits/docs/traits.md deleted file mode 100644 index fa0a3254b..000000000 --- a/projects/traits/docs/traits.md +++ /dev/null @@ -1,114 +0,0 @@ - -# traits - - -**metamodel version:** 1.7.0 - -**version:** None - - -A template for Traits - - -### Classes - - * [AnnotatorResult](AnnotatorResult.md) - * [Any](Any.md) - * [CompoundExpression](CompoundExpression.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - * [ExtractionResult](ExtractionResult.md) - A result of extracting knowledge on text - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Trait](Trait.md) - * [Publication](Publication.md) - * [Taxon](Taxon.md) - * [TextWithTriples](TextWithTriples.md) - -### Mixins - - -### Slots - - * [➞object_id](annotatorResult__object_id.md) - * [➞object_text](annotatorResult__object_text.md) - * [➞subject_text](annotatorResult__subject_text.md) - * [➞extracted_object](extractionResult__extracted_object.md) - The complex objects extracted from the text - * [➞input_id](extractionResult__input_id.md) - * [➞input_text](extractionResult__input_text.md) - * [➞input_title](extractionResult__input_title.md) - * [➞named_entities](extractionResult__named_entities.md) - Named entities extracted from the text - * [➞prompt](extractionResult__prompt.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) - * [➞id](namedEntity__id.md) - A unique identifier for the named entity - * [➞label](namedEntity__label.md) - The label (name) of the named thing - * [➞abstract](publication__abstract.md) - The abstract of the publication - * [➞combined_text](publication__combined_text.md) - * [➞full_text](publication__full_text.md) - The full text of the publication - * [➞id](publication__id.md) - The publication identifier - * [➞title](publication__title.md) - The title of the publication - * [➞cellular_traits](taxon__cellular_traits.md) - The cellular traits for the taxon. - * [➞ecological_traits](taxon__ecological_traits.md) - The ecological traits for the taxon. - * [➞genetic_traits](taxon__genetic_traits.md) - The genetic traits for the taxon. - * [➞metabolic_traits](taxon__metabolic_traits.md) - The metabolic traits for the taxon. - * [➞morphological_traits](taxon__morphological_traits.md) - The morphological traits for the taxon. - * [➞phenotypic_plasticiticy_traits](taxon__phenotypic_plasticiticy_traits.md) - The phenotypic plasticiticy traits for the taxon. - * [➞preferred_environments](taxon__preferred_environments.md) - The preferred environments for the taxon. - * [➞reproductive_traits](taxon__reproductive_traits.md) - The reproductive traits for the taxon. - * [➞survival_traits](taxon__survival_traits.md) - The survival traits for the taxon. - * [➞publication](textWithTriples__publication.md) - * [➞triples](textWithTriples__triples.md) - * [➞object](triple__object.md) - * [➞object_qualifier](triple__object_qualifier.md) - An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * [➞predicate](triple__predicate.md) - * [➞qualifier](triple__qualifier.md) - A qualifier for the statements, e.g. "NOT" for negation - * [➞subject](triple__subject.md) - * [➞subject_qualifier](triple__subject_qualifier.md) - An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -### Enums - - * [NullDataOptions](NullDataOptions.md) - -### Subsets - - -### Types - - -#### Built in - - * **Bool** - * **Curie** - * **Decimal** - * **ElementIdentifier** - * **NCName** - * **NodeIdentifier** - * **URI** - * **URIorCURIE** - * **XSDDate** - * **XSDDateTime** - * **XSDTime** - * **float** - * **int** - * **str** - -#### Defined - - * [Boolean](types/Boolean.md) (**Bool**) - A binary (true or false) value - * [Curie](types/Curie.md) (**Curie**) - a compact URI - * [Date](types/Date.md) (**XSDDate**) - a date (year, month and day) in an idealized calendar - * [DateOrDatetime](types/DateOrDatetime.md) (**str**) - Either a date or a datetime - * [Datetime](types/Datetime.md) (**XSDDateTime**) - The combination of a date and time - * [Decimal](types/Decimal.md) (**Decimal**) - A real number with arbitrary precision that conforms to the xsd:decimal specification - * [Double](types/Double.md) (**float**) - A real number that conforms to the xsd:double specification - * [Float](types/Float.md) (**float**) - A real number that conforms to the xsd:float specification - * [Integer](types/Integer.md) (**int**) - An integer - * [Jsonpath](types/Jsonpath.md) (**str**) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - * [Jsonpointer](types/Jsonpointer.md) (**str**) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - * [Ncname](types/Ncname.md) (**NCName**) - Prefix part of CURIE - * [Nodeidentifier](types/Nodeidentifier.md) (**NodeIdentifier**) - A URI, CURIE or BNODE that represents a node in a model. - * [Objectidentifier](types/Objectidentifier.md) (**ElementIdentifier**) - A URI or CURIE that represents an object in the model. - * [Sparqlpath](types/Sparqlpath.md) (**str**) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - * [String](types/String.md) (**str**) - A character string - * [Time](types/Time.md) (**XSDTime**) - A time object represents a (local) time of day, independent of any particular day - * [Uri](types/Uri.md) (**URI**) - a complete URI - * [Uriorcurie](types/Uriorcurie.md) (**URIorCURIE**) - a URI or a CURIE diff --git a/projects/traits/docs/triple__object.md b/projects/traits/docs/triple__object.md deleted file mode 100644 index 7b2fa004f..000000000 --- a/projects/traits/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [traits:triple__object](http://w3id.org/ontogpt/traits/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/traits/docs/triple__object_qualifier.md b/projects/traits/docs/triple__object_qualifier.md deleted file mode 100644 index bbafc0ff9..000000000 --- a/projects/traits/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [traits:triple__object_qualifier](http://w3id.org/ontogpt/traits/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/traits/docs/triple__predicate.md b/projects/traits/docs/triple__predicate.md deleted file mode 100644 index 5ba49bb44..000000000 --- a/projects/traits/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [traits:triple__predicate](http://w3id.org/ontogpt/traits/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/traits/docs/triple__qualifier.md b/projects/traits/docs/triple__qualifier.md deleted file mode 100644 index 7acc93a88..000000000 --- a/projects/traits/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [traits:triple__qualifier](http://w3id.org/ontogpt/traits/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/traits/docs/triple__subject.md b/projects/traits/docs/triple__subject.md deleted file mode 100644 index 3de81a682..000000000 --- a/projects/traits/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [traits:triple__subject](http://w3id.org/ontogpt/traits/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/traits/docs/triple__subject_qualifier.md b/projects/traits/docs/triple__subject_qualifier.md deleted file mode 100644 index d5adf9d53..000000000 --- a/projects/traits/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [traits:triple__subject_qualifier](http://w3id.org/ontogpt/traits/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/traits/docs/types/Boolean.md b/projects/traits/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/traits/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/traits/docs/types/Curie.md b/projects/traits/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/traits/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/traits/docs/types/Date.md b/projects/traits/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/traits/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/traits/docs/types/DateOrDatetime.md b/projects/traits/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/traits/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/traits/docs/types/Datetime.md b/projects/traits/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/traits/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/traits/docs/types/Decimal.md b/projects/traits/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/traits/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/traits/docs/types/Double.md b/projects/traits/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/traits/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/traits/docs/types/Float.md b/projects/traits/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/traits/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/traits/docs/types/Integer.md b/projects/traits/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/traits/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/traits/docs/types/Jsonpath.md b/projects/traits/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/traits/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/traits/docs/types/Jsonpointer.md b/projects/traits/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/traits/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/traits/docs/types/Ncname.md b/projects/traits/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/traits/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/traits/docs/types/Nodeidentifier.md b/projects/traits/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/traits/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/traits/docs/types/Objectidentifier.md b/projects/traits/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/traits/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/traits/docs/types/Sparqlpath.md b/projects/traits/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/traits/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/traits/docs/types/String.md b/projects/traits/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/traits/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/traits/docs/types/Time.md b/projects/traits/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/traits/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/traits/docs/types/Uri.md b/projects/traits/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/traits/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/traits/docs/types/Uriorcurie.md b/projects/traits/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/traits/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/traits/excel/traits.xlsx b/projects/traits/excel/traits.xlsx deleted file mode 100644 index b5f20503482e02c4984246ca8999a82e8b5ad2e0..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 8318 zcmeHtbx@Sy*Y;A<-AhYKcXx-BbazU3cS$!&HzKKYNOyNFB_SXnrF49&e(&o~KArhy z-hbbnd7hnTX3w?vUgzBBT<1QkBnJhJ1polx0O%U98j{+bNI~GI_uvZ+e3{ytC^^|X zI5QbJI52wH+Q`SsBX%*Pi9g8ht=Op@ld_P`6s!+=OLK9?n~J%G-ukF?#)0@(nWLMr 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morphologicalTraits: [Trait] - geneticTraits: [Trait] - cellularTraits: [Trait] - ecologicalTraits: [Trait] - reproductiveTraits: [Trait] - survivalTraits: [Trait] - phenotypicPlasticiticyTraits: [Trait] - preferredEnvironments: [Trait] - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -type Trait - { - id: String! - label: String - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/traits/jsonld/traits.context.jsonld b/projects/traits/jsonld/traits.context.jsonld deleted file mode 100644 index bb4e529fe..000000000 --- a/projects/traits/jsonld/traits.context.jsonld +++ /dev/null @@ -1,159 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:56:23", - "source": "traits.yaml" - }, - "@context": { - "BIODIVTHES": "http://example.org/UNKNOWN/BIODIVTHES/", - "ECOCORE": "http://example.org/UNKNOWN/ECOCORE/", - "GO": "http://example.org/UNKNOWN/GO/", - "OBA": "http://example.org/UNKNOWN/OBA/", - "PATO": "http://example.org/UNKNOWN/PATO/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "traits": "http://w3id.org/ontogpt/traits/", - "@vocab": "http://w3id.org/ontogpt/traits/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "cellular_traits": { - "@type": "@id" - }, - "ecological_traits": { - "@type": "@id" - }, - "genetic_traits": { - "@type": "@id" - }, - "metabolic_traits": { - "@type": "@id" - }, - "morphological_traits": { - "@type": "@id" - }, - "phenotypic_plasticiticy_traits": { - "@type": "@id" - }, - "preferred_environments": { - "@type": "@id" - }, - "reproductive_traits": { - "@type": "@id" - }, - "survival_traits": { - "@type": "@id" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/traits/jsonld/traits.jsonld b/projects/traits/jsonld/traits.jsonld deleted file mode 100644 index 0bd832b53..000000000 --- a/projects/traits/jsonld/traits.jsonld +++ /dev/null @@ -1,1335 +0,0 @@ -{ - "name": "traits", - "description": "A template for Traits", - "title": "Traits Template", - "id": "http://w3id.org/ontogpt/traits", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "traits", - "prefix_reference": "http://w3id.org/ontogpt/traits/" - } - ], - "default_prefix": "traits", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "taxon__metabolic_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism metabolic trait", - "@type": "Annotation" - } - ], - "description": "The metabolic traits for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/metabolic_traits", - "multivalued": true, - "alias": "metabolic_traits", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "taxon__morphological_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism morphological trait", - "@type": "Annotation" - } - ], - "description": "The morphological traits for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/morphological_traits", - "multivalued": true, - "alias": "morphological_traits", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "taxon__genetic_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism genetic trait", - "@type": "Annotation" - } - ], - "description": "The genetic traits for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/genetic_traits", - "multivalued": true, - "alias": "genetic_traits", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "taxon__cellular_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism cellular trait", - "@type": "Annotation" - } - ], - "description": "The cellular traits for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/cellular_traits", - "multivalued": true, - "alias": "cellular_traits", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "taxon__ecological_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism ecological trait", - "@type": "Annotation" - } - ], - "description": "The ecological traits for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/ecological_traits", - "multivalued": true, - "alias": "ecological_traits", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "taxon__reproductive_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism reproductive trait", - "@type": "Annotation" - } - ], - "description": "The reproductive traits for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/reproductive_traits", - "multivalued": true, - "alias": "reproductive_traits", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "taxon__survival_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism survival trait", - "@type": "Annotation" - } - ], - "description": "The survival traits for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/survival_traits", - "multivalued": true, - "alias": "survival_traits", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "taxon__phenotypic_plasticiticy_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism phenotypic plasticiticy trait", - "@type": "Annotation" - } - ], - "description": "The phenotypic plasticiticy traits for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/phenotypic_plasticiticy_traits", - "multivalued": true, - "alias": "phenotypic_plasticiticy_traits", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "taxon__preferred_environments", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of the environments the organism is typically found in or isolated from", - "@type": "Annotation" - } - ], - "description": "The preferred environments for the taxon.", - "from_schema": "http://w3id.org/ontogpt/traits", - "slot_uri": "http://w3id.org/ontogpt/traits/preferred_environments", - "multivalued": true, - "alias": "preferred_environments", - "owner": "Taxon", - "domain_of": [ - "Taxon" - ], - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "Taxon", - "definition_uri": "http://w3id.org/ontogpt/traits/Taxon", - "from_schema": "http://w3id.org/ontogpt/traits", - "slots": [ - "taxon__metabolic_traits", - "taxon__morphological_traits", - "taxon__genetic_traits", - "taxon__cellular_traits", - "taxon__ecological_traits", - "taxon__reproductive_traits", - "taxon__survival_traits", - "taxon__phenotypic_plasticiticy_traits", - "taxon__preferred_environments" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "metabolic_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism metabolic trait", - "@type": "Annotation" - } - ], - "description": "The metabolic traits for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "morphological_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism morphological trait", - "@type": "Annotation" - } - ], - "description": "The morphological traits for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "genetic_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism genetic trait", - "@type": "Annotation" - } - ], - "description": "The genetic traits for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "cellular_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism cellular trait", - "@type": "Annotation" - } - ], - "description": "The cellular traits for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "ecological_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism ecological trait", - "@type": "Annotation" - } - ], - "description": "The ecological traits for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "reproductive_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism reproductive trait", - "@type": "Annotation" - } - ], - "description": "The reproductive traits for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "survival_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism survival trait", - "@type": "Annotation" - } - ], - "description": "The survival traits for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "phenotypic_plasticiticy_traits", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of every specific organism phenotypic plasticiticy trait", - "@type": "Annotation" - } - ], - "description": "The phenotypic plasticiticy traits for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - }, - { - "name": "preferred_environments", - "annotations": [ - { - "tag": "prompt", - "value": "a semicolon separated list of the environments the organism is typically found in or isolated from", - "@type": "Annotation" - } - ], - "description": "The preferred environments for the taxon.", - "multivalued": true, - "range": "Trait", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/traits/Taxon", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Trait", - "id_prefixes": [ - "ECOCORE", - "PATO", - "GO", - "OBA", - "BIODIVTHES" - ], - "definition_uri": "http://w3id.org/ontogpt/traits/Trait", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:ecocore, sqlite:obo:pato, sqlite:obo:go, sqlite:obo:oba, bioportal:biodivthes", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/traits", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/traits/Trait", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "traits.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 3502, - "generation_date": "2023-08-07T10:56:24", - "@type": "SchemaDefinition", - "@context": [ - "projects/traits/jsonld/traits.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/traits/" - } - ] -} diff --git a/projects/traits/jsonschema/traits.schema.json b/projects/traits/jsonschema/traits.schema.json deleted file mode 100644 index 088b349a4..000000000 --- a/projects/traits/jsonschema/traits.schema.json +++ /dev/null @@ -1,296 +0,0 @@ -{ - "$defs": { - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "Taxon": { - "additionalProperties": false, - "description": "", - "properties": { - "cellular_traits": { - "description": "The cellular traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "ecological_traits": { - "description": "The ecological traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "genetic_traits": { - "description": "The genetic traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "metabolic_traits": { - "description": "The metabolic traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "morphological_traits": { - "description": "The morphological traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "phenotypic_plasticiticy_traits": { - "description": "The phenotypic plasticiticy traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "preferred_environments": { - "description": "The preferred environments for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "reproductive_traits": { - "description": "The reproductive traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "survival_traits": { - "description": "The survival traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "Taxon", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Trait": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Trait", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/traits", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "cellular_traits": { - "description": "The cellular traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "ecological_traits": { - "description": "The ecological traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "genetic_traits": { - "description": "The genetic traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "metabolic_traits": { - "description": "The metabolic traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "morphological_traits": { - "description": "The morphological traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "phenotypic_plasticiticy_traits": { - "description": "The phenotypic plasticiticy traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "preferred_environments": { - "description": "The preferred environments for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "reproductive_traits": { - "description": "The reproductive traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - }, - "survival_traits": { - "description": "The survival traits for the taxon.", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "traits", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/traits/owl/traits.owl.ttl b/projects/traits/owl/traits.owl.ttl deleted file mode 100644 index 1b531ac3a..000000000 --- a/projects/traits/owl/traits.owl.ttl +++ /dev/null @@ -1,457 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix traits: <http://w3id.org/ontogpt/traits/> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/traits> a owl:Ontology ; - rdfs:label "traits" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - traits:Taxon ; - linkml:classes "{'Taxon': ClassDefinition(name='Taxon', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/traits/Taxon', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/traits', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['taxon__metabolic_traits', 'taxon__morphological_traits', 'taxon__genetic_traits', 'taxon__cellular_traits', 'taxon__ecological_traits', 'taxon__reproductive_traits', 'taxon__survival_traits', 'taxon__phenotypic_plasticiticy_traits', 'taxon__preferred_environments'], slot_usage={}, attributes={'metabolic_traits': SlotDefinition(name='metabolic_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism metabolic trait', extensions={}, annotations={})}, description='The metabolic traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'morphological_traits': SlotDefinition(name='morphological_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism morphological trait', extensions={}, annotations={})}, description='The morphological traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'genetic_traits': SlotDefinition(name='genetic_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism genetic trait', extensions={}, annotations={})}, description='The genetic traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'cellular_traits': SlotDefinition(name='cellular_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism cellular trait', extensions={}, annotations={})}, description='The cellular traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ecological_traits': SlotDefinition(name='ecological_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism ecological trait', extensions={}, annotations={})}, description='The ecological traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'reproductive_traits': SlotDefinition(name='reproductive_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism reproductive trait', extensions={}, annotations={})}, description='The reproductive traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'survival_traits': SlotDefinition(name='survival_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism survival trait', extensions={}, annotations={})}, description='The survival traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'phenotypic_plasticiticy_traits': SlotDefinition(name='phenotypic_plasticiticy_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism phenotypic plasticiticy trait', extensions={}, annotations={})}, description='The phenotypic plasticiticy traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'preferred_environments': SlotDefinition(name='preferred_environments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of the environments the organism is typically found in or isolated from', extensions={}, annotations={})}, description='The preferred environments for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='traits:Taxon', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Trait': ClassDefinition(name='Trait', id_prefixes=['ECOCORE', 'PATO', 'GO', 'OBA', 'BIODIVTHES'], definition_uri='http://w3id.org/ontogpt/traits/Trait', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:ecocore, sqlite:obo:pato, sqlite:obo:go, sqlite:obo:oba, bioportal:biodivthes', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/traits', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='traits:Trait', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/traits" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - traits:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -traits:Taxon a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Taxon" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:genetic_traits ], - [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:phenotypic_plasticiticy_traits ], - [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:cellular_traits ], - [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:preferred_environments ], - [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:ecological_traits ], - [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:reproductive_traits ], - [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:survival_traits ], - [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:metabolic_traits ], - [ a owl:Restriction ; - owl:allValuesFrom traits:Trait ; - owl:onProperty traits:morphological_traits ] ; - linkml:attributes "{'metabolic_traits': SlotDefinition(name='metabolic_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism metabolic trait', extensions={}, annotations={})}, description='The metabolic traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'morphological_traits': SlotDefinition(name='morphological_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism morphological trait', extensions={}, annotations={})}, description='The morphological traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'genetic_traits': SlotDefinition(name='genetic_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism genetic trait', extensions={}, annotations={})}, description='The genetic traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'cellular_traits': SlotDefinition(name='cellular_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism cellular trait', extensions={}, annotations={})}, description='The cellular traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ecological_traits': SlotDefinition(name='ecological_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism ecological trait', extensions={}, annotations={})}, description='The ecological traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'reproductive_traits': SlotDefinition(name='reproductive_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism reproductive trait', extensions={}, annotations={})}, description='The reproductive traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'survival_traits': SlotDefinition(name='survival_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism survival trait', extensions={}, annotations={})}, description='The survival traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'phenotypic_plasticiticy_traits': SlotDefinition(name='phenotypic_plasticiticy_traits', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of every specific organism phenotypic plasticiticy trait', extensions={}, annotations={})}, description='The phenotypic plasticiticy traits for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'preferred_environments': SlotDefinition(name='preferred_environments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt': Annotation(tag='prompt', value='a semicolon separated list of the environments the organism is typically found in or isolated from', extensions={}, annotations={})}, description='The preferred environments for the taxon.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Trait', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -traits:cellular_traits a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "cellular_traits" ; - traits:prompt "a semicolon separated list of every specific organism cellular trait" ; - rdfs:range traits:Trait ; - skos:definition "The cellular traits for the taxon." . - -traits:ecological_traits a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "ecological_traits" ; - traits:prompt "a semicolon separated list of every specific organism ecological trait" ; - rdfs:range traits:Trait ; - skos:definition "The ecological traits for the taxon." . - -traits:genetic_traits a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "genetic_traits" ; - traits:prompt "a semicolon separated list of every specific organism genetic trait" ; - rdfs:range traits:Trait ; - skos:definition "The genetic traits for the taxon." . - -traits:metabolic_traits a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "metabolic_traits" ; - traits:prompt "a semicolon separated list of every specific organism metabolic trait" ; - rdfs:range traits:Trait ; - skos:definition "The metabolic traits for the taxon." . - -traits:morphological_traits a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "morphological_traits" ; - traits:prompt "a semicolon separated list of every specific organism morphological trait" ; - rdfs:range traits:Trait ; - skos:definition "The morphological traits for the taxon." . - -traits:phenotypic_plasticiticy_traits a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "phenotypic_plasticiticy_traits" ; - traits:prompt "a semicolon separated list of every specific organism phenotypic plasticiticy trait" ; - rdfs:range traits:Trait ; - skos:definition "The phenotypic plasticiticy traits for the taxon." . - -traits:preferred_environments a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "preferred_environments" ; - traits:prompt "a semicolon separated list of the environments the organism is typically found in or isolated from" ; - rdfs:range traits:Trait ; - skos:definition "The preferred environments for the taxon." . - -traits:reproductive_traits a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "reproductive_traits" ; - traits:prompt "a semicolon separated list of every specific organism reproductive trait" ; - rdfs:range traits:Trait ; - skos:definition "The reproductive traits for the taxon." . - -traits:survival_traits a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "survival_traits" ; - traits:prompt "a semicolon separated list of every specific organism survival trait" ; - rdfs:range traits:Trait ; - skos:definition "The survival traits for the taxon." . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - traits:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -traits:Trait a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Trait" ; - traits:annotators "sqlite:obo:ecocore, sqlite:obo:pato, sqlite:obo:go, sqlite:obo:oba, bioportal:biodivthes" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/traits/prefixmap/traits.yaml b/projects/traits/prefixmap/traits.yaml deleted file mode 100644 index 8b9ce761a..000000000 --- a/projects/traits/prefixmap/traits.yaml +++ /dev/null @@ -1,40 +0,0 @@ -{ - "BIODIVTHES": "http://example.org/UNKNOWN/BIODIVTHES/", - "ECOCORE": "http://example.org/UNKNOWN/ECOCORE/", - "GO": "http://example.org/UNKNOWN/GO/", - "OBA": "http://example.org/UNKNOWN/OBA/", - "PATO": "http://example.org/UNKNOWN/PATO/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "traits": "http://w3id.org/ontogpt/traits/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/traits/protobuf/traits.proto b/projects/traits/protobuf/traits.proto deleted file mode 100644 index 8cfeb2c3e..000000000 --- a/projects/traits/protobuf/traits.proto +++ /dev/null @@ -1,52 +0,0 @@ -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message Taxon - { - repeated trait metabolicTraits = 0 - repeated trait morphologicalTraits = 0 - repeated trait geneticTraits = 0 - repeated trait cellularTraits = 0 - repeated trait ecologicalTraits = 0 - repeated trait reproductiveTraits = 0 - repeated trait survivalTraits = 0 - repeated trait phenotypicPlasticiticyTraits = 0 - repeated trait preferredEnvironments = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Trait - { - string id = 0 - string label = 0 - } diff --git a/projects/traits/shacl/traits.shacl.ttl b/projects/traits/shacl/traits.shacl.ttl deleted file mode 100644 index 89f18885e..000000000 --- a/projects/traits/shacl/traits.shacl.ttl +++ /dev/null @@ -1,228 +0,0 @@ -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix traits: <http://w3id.org/ontogpt/traits/> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -traits:Taxon a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class traits:Trait ; - sh:description "The cellular traits for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path traits:cellular_traits ], - [ sh:class traits:Trait ; - sh:description "The survival traits for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path traits:survival_traits ], - [ sh:class traits:Trait ; - sh:description "The genetic traits for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path traits:genetic_traits ], - [ sh:class traits:Trait ; - sh:description "The reproductive traits for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path traits:reproductive_traits ], - [ sh:class traits:Trait ; - sh:description "The preferred environments for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path traits:preferred_environments ], - [ sh:class traits:Trait ; - sh:description "The ecological traits for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path traits:ecological_traits ], - [ sh:class traits:Trait ; - sh:description "The morphological traits for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path traits:morphological_traits ], - [ sh:class traits:Trait ; - sh:description "The phenotypic plasticiticy traits for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path traits:phenotypic_plasticiticy_traits ], - [ sh:class traits:Trait ; - sh:description "The metabolic traits for the taxon." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path traits:metabolic_traits ] ; - sh:targetClass traits:Taxon . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ], - [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - -traits:Trait a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass traits:Trait . - diff --git a/projects/traits/shex/traits.shex b/projects/traits/shex/traits.shex deleted file mode 100644 index 12c6ec8da..000000000 --- a/projects/traits/shex/traits.shex +++ /dev/null @@ -1,157 +0,0 @@ -BASE <http://w3id.org/ontogpt/traits/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) - } OR @core:Triple -) - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -core:NamedEntity ( - @core:RelationshipType OR @<Trait> -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -<Taxon> CLOSED { - ( $<Taxon_tes> ( <metabolic_traits> @<Trait> * ; - <morphological_traits> @<Trait> * ; - <genetic_traits> @<Trait> * ; - <cellular_traits> @<Trait> * ; - <ecological_traits> @<Trait> * ; - <reproductive_traits> @<Trait> * ; - <survival_traits> @<Trait> * ; - <phenotypic_plasticiticy_traits> @<Trait> * ; - <preferred_environments> @<Trait> * - ) ; - rdf:type [ <Taxon> ] ? - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -<Trait> CLOSED { - ( $<Trait_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Trait> ] - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/traits/sqlschema/traits.sql b/projects/traits/sqlschema/traits.sql deleted file mode 100644 index 36ce87d04..000000000 --- a/projects/traits/sqlschema/traits.sql +++ /dev/null @@ -1,59 +0,0 @@ - - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Taxon" ( - metabolic_traits TEXT, - morphological_traits TEXT, - genetic_traits TEXT, - cellular_traits TEXT, - ecological_traits TEXT, - reproductive_traits TEXT, - survival_traits TEXT, - phenotypic_plasticiticy_traits TEXT, - preferred_environments TEXT, - PRIMARY KEY (metabolic_traits, morphological_traits, genetic_traits, cellular_traits, ecological_traits, reproductive_traits, survival_traits, phenotypic_plasticiticy_traits, preferred_environments) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Trait" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); diff --git a/projects/traits/traits.py b/projects/traits/traits.py deleted file mode 100644 index 1719ab9f9..000000000 --- a/projects/traits/traits.py +++ /dev/null @@ -1,477 +0,0 @@ -# Auto generated from traits.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:56:31 -# Schema: traits -# -# id: http://w3id.org/ontogpt/traits -# description: A template for Traits -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -BIODIVTHES = CurieNamespace('BIODIVTHES', 'http://example.org/UNKNOWN/BIODIVTHES/') -ECOCORE = CurieNamespace('ECOCORE', 'http://example.org/UNKNOWN/ECOCORE/') -GO = CurieNamespace('GO', 'http://example.org/UNKNOWN/GO/') -OBA = CurieNamespace('OBA', 'http://example.org/UNKNOWN/OBA/') -PATO = CurieNamespace('PATO', 'http://example.org/UNKNOWN/PATO/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -TRAITS = CurieNamespace('traits', 'http://w3id.org/ontogpt/traits/') -DEFAULT_ = TRAITS - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class TraitId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class Taxon(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TRAITS.Taxon - class_class_curie: ClassVar[str] = "traits:Taxon" - class_name: ClassVar[str] = "Taxon" - class_model_uri: ClassVar[URIRef] = TRAITS.Taxon - - metabolic_traits: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - morphological_traits: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - genetic_traits: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - cellular_traits: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - ecological_traits: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - reproductive_traits: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - survival_traits: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - phenotypic_plasticiticy_traits: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - preferred_environments: Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if not isinstance(self.metabolic_traits, list): - self.metabolic_traits = [self.metabolic_traits] if self.metabolic_traits is not None else [] - self.metabolic_traits = [v if isinstance(v, TraitId) else TraitId(v) for v in self.metabolic_traits] - - if not isinstance(self.morphological_traits, list): - self.morphological_traits = [self.morphological_traits] if self.morphological_traits is not None else [] - self.morphological_traits = [v if isinstance(v, TraitId) else TraitId(v) for v in self.morphological_traits] - - if not isinstance(self.genetic_traits, list): - self.genetic_traits = [self.genetic_traits] if self.genetic_traits is not None else [] - self.genetic_traits = [v if isinstance(v, TraitId) else TraitId(v) for v in self.genetic_traits] - - if not isinstance(self.cellular_traits, list): - self.cellular_traits = [self.cellular_traits] if self.cellular_traits is not None else [] - self.cellular_traits = [v if isinstance(v, TraitId) else TraitId(v) for v in self.cellular_traits] - - if not isinstance(self.ecological_traits, list): - self.ecological_traits = [self.ecological_traits] if self.ecological_traits is not None else [] - self.ecological_traits = [v if isinstance(v, TraitId) else TraitId(v) for v in self.ecological_traits] - - if not isinstance(self.reproductive_traits, list): - self.reproductive_traits = [self.reproductive_traits] if self.reproductive_traits is not None else [] - self.reproductive_traits = [v if isinstance(v, TraitId) else TraitId(v) for v in self.reproductive_traits] - - if not isinstance(self.survival_traits, list): - self.survival_traits = [self.survival_traits] if self.survival_traits is not None else [] - self.survival_traits = [v if isinstance(v, TraitId) else TraitId(v) for v in self.survival_traits] - - if not isinstance(self.phenotypic_plasticiticy_traits, list): - self.phenotypic_plasticiticy_traits = [self.phenotypic_plasticiticy_traits] if self.phenotypic_plasticiticy_traits is not None else [] - self.phenotypic_plasticiticy_traits = [v if isinstance(v, TraitId) else TraitId(v) for v in self.phenotypic_plasticiticy_traits] - - if not isinstance(self.preferred_environments, list): - self.preferred_environments = [self.preferred_environments] if self.preferred_environments is not None else [] - self.preferred_environments = [v if isinstance(v, TraitId) else TraitId(v) for v in self.preferred_environments] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = TRAITS.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = TRAITS.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Trait(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TRAITS.Trait - class_class_curie: ClassVar[str] = "traits:Trait" - class_name: ClassVar[str] = "Trait" - class_model_uri: ClassVar[URIRef] = TRAITS.Trait - - id: Union[str, TraitId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, TraitId): - self.id = TraitId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = TRAITS.CompoundExpression - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = TRAITS.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = TRAITS.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = TRAITS.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = TRAITS.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = TRAITS.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.taxon__metabolic_traits = Slot(uri=TRAITS.metabolic_traits, name="taxon__metabolic_traits", curie=TRAITS.curie('metabolic_traits'), - model_uri=TRAITS.taxon__metabolic_traits, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.taxon__morphological_traits = Slot(uri=TRAITS.morphological_traits, name="taxon__morphological_traits", curie=TRAITS.curie('morphological_traits'), - model_uri=TRAITS.taxon__morphological_traits, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.taxon__genetic_traits = Slot(uri=TRAITS.genetic_traits, name="taxon__genetic_traits", curie=TRAITS.curie('genetic_traits'), - model_uri=TRAITS.taxon__genetic_traits, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.taxon__cellular_traits = Slot(uri=TRAITS.cellular_traits, name="taxon__cellular_traits", curie=TRAITS.curie('cellular_traits'), - model_uri=TRAITS.taxon__cellular_traits, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.taxon__ecological_traits = Slot(uri=TRAITS.ecological_traits, name="taxon__ecological_traits", curie=TRAITS.curie('ecological_traits'), - model_uri=TRAITS.taxon__ecological_traits, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.taxon__reproductive_traits = Slot(uri=TRAITS.reproductive_traits, name="taxon__reproductive_traits", curie=TRAITS.curie('reproductive_traits'), - model_uri=TRAITS.taxon__reproductive_traits, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.taxon__survival_traits = Slot(uri=TRAITS.survival_traits, name="taxon__survival_traits", curie=TRAITS.curie('survival_traits'), - model_uri=TRAITS.taxon__survival_traits, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.taxon__phenotypic_plasticiticy_traits = Slot(uri=TRAITS.phenotypic_plasticiticy_traits, name="taxon__phenotypic_plasticiticy_traits", curie=TRAITS.curie('phenotypic_plasticiticy_traits'), - model_uri=TRAITS.taxon__phenotypic_plasticiticy_traits, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.taxon__preferred_environments = Slot(uri=TRAITS.preferred_environments, name="taxon__preferred_environments", curie=TRAITS.curie('preferred_environments'), - model_uri=TRAITS.taxon__preferred_environments, domain=None, range=Optional[Union[Union[str, TraitId], List[Union[str, TraitId]]]]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=TRAITS.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=TRAITS.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=TRAITS.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=TRAITS.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=TRAITS.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=TRAITS.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=TRAITS.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=TRAITS.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=TRAITS.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=TRAITS.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=TRAITS.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=TRAITS.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=TRAITS.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=TRAITS.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=TRAITS.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=TRAITS.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=TRAITS.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=TRAITS.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=TRAITS.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=TRAITS.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=TRAITS.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=TRAITS.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=TRAITS.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=TRAITS.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=TRAITS.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file diff --git a/projects/treatment/docs/AdverseEffect.md b/projects/treatment/docs/AdverseEffect.md deleted file mode 100644 index 8242cd541..000000000 --- a/projects/treatment/docs/AdverseEffect.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: AdverseEffect - - - - -URI: [treatment:AdverseEffect](http://w3id.org/ontogpt/treatments/AdverseEffect) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[TreatmentAdverseEffect]-%20adverse_effects%200..*>[AdverseEffect|id(i):string;label(i):string%20%3F],[NamedEntity]^-[AdverseEffect],[TreatmentAdverseEffect])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[TreatmentAdverseEffect]-%20adverse_effects%200..*>[AdverseEffect|id(i):string;label(i):string%20%3F],[NamedEntity]^-[AdverseEffect],[TreatmentAdverseEffect]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞adverse_effects](treatmentAdverseEffect__adverse_effects.md)* <sub>0..\*</sub> **[AdverseEffect](AdverseEffect.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/AnnotatorResult.md b/projects/treatment/docs/AnnotatorResult.md deleted file mode 100644 index bc9629fcf..000000000 --- a/projects/treatment/docs/AnnotatorResult.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Class: AnnotatorResult - - - - -URI: [treatment:AnnotatorResult](http://w3id.org/ontogpt/treatments/AnnotatorResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[AnnotatorResult|subject_text:string%20%3F;object_id:string%20%3F;object_text:string%20%3F]) - -## Attributes - - -### Own - - * [➞subject_text](annotatorResult__subject_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_id](annotatorResult__object_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞object_text](annotatorResult__object_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/Any.md b/projects/treatment/docs/Any.md deleted file mode 100644 index 9abde1382..000000000 --- a/projects/treatment/docs/Any.md +++ /dev/null @@ -1,25 +0,0 @@ - -# Class: Any - - - - -URI: [treatment:Any](http://w3id.org/ontogpt/treatments/Any) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult])](https://yuml.me/diagram/nofunky;dir:TB/class/[ExtractionResult]++-%20extracted_object%200..1>[Any],[ExtractionResult]++-%20named_entities%200..*>[Any],[ExtractionResult]) - -## Referenced by Class - - * **None** *[➞extracted_object](extractionResult__extracted_object.md)* <sub>0..1</sub> **[Any](Any.md)** - * **None** *[➞named_entities](extractionResult__named_entities.md)* <sub>0..\*</sub> **[Any](Any.md)** - -## Attributes - - -## Other properties - -| | | | -| --- | --- | --- | -| **Mappings:** | | linkml:Any | - diff --git a/projects/treatment/docs/CHEBIDrugType.md b/projects/treatment/docs/CHEBIDrugType.md deleted file mode 100644 index a3ad7a5ad..000000000 --- a/projects/treatment/docs/CHEBIDrugType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: CHEBIDrugType - - - - -URI: [treatment:CHEBIDrugType](http://w3id.org/ontogpt/treatments/CHEBIDrugType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/treatment/docs/CompoundExpression.md b/projects/treatment/docs/CompoundExpression.md deleted file mode 100644 index f4039af7f..000000000 --- a/projects/treatment/docs/CompoundExpression.md +++ /dev/null @@ -1,23 +0,0 @@ - -# Class: CompoundExpression - - - - -URI: [treatment:CompoundExpression](http://w3id.org/ontogpt/treatments/CompoundExpression) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[CompoundExpression]^-[Triple],[CompoundExpression]^-[TreatmentMechanism],[CompoundExpression]^-[TreatmentEfficacy],[CompoundExpression]^-[TreatmentAdverseEffect])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[CompoundExpression]^-[Triple],[CompoundExpression]^-[TreatmentMechanism],[CompoundExpression]^-[TreatmentEfficacy],[CompoundExpression]^-[TreatmentAdverseEffect]) - -## Children - - * [TreatmentAdverseEffect](TreatmentAdverseEffect.md) - * [TreatmentEfficacy](TreatmentEfficacy.md) - * [TreatmentMechanism](TreatmentMechanism.md) - * [Triple](Triple.md) - Abstract parent for Relation Extraction tasks - -## Referenced by Class - - -## Attributes - diff --git a/projects/treatment/docs/Disease.md b/projects/treatment/docs/Disease.md deleted file mode 100644 index 4b0212050..000000000 --- a/projects/treatment/docs/Disease.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Disease - - - - -URI: [treatment:Disease](http://w3id.org/ontogpt/treatments/Disease) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiseaseTreatmentSummary]-%20disease%200..1>[Disease|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Disease],[DiseaseTreatmentSummary])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiseaseTreatmentSummary]-%20disease%200..1>[Disease|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Disease],[DiseaseTreatmentSummary]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞disease](diseaseTreatmentSummary__disease.md)* <sub>0..1</sub> **[Disease](Disease.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/DiseaseTreatmentSummary.md b/projects/treatment/docs/DiseaseTreatmentSummary.md deleted file mode 100644 index 7291c8464..000000000 --- a/projects/treatment/docs/DiseaseTreatmentSummary.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Class: DiseaseTreatmentSummary - - - - -URI: [treatment:DiseaseTreatmentSummary](http://w3id.org/ontogpt/treatments/DiseaseTreatmentSummary) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[Treatment],[Drug],[TreatmentAdverseEffect]<treatment_adverse_effects%200..*-++[DiseaseTreatmentSummary],[TreatmentEfficacy]<treatment_efficacies%200..*-++[DiseaseTreatmentSummary],[TreatmentMechanism]<treatment_mechanisms%200..*-++[DiseaseTreatmentSummary],[Treatment]<contraindications%200..*-%20[DiseaseTreatmentSummary],[Treatment]<treatments%200..*-%20[DiseaseTreatmentSummary],[Drug]<drugs%200..*-%20[DiseaseTreatmentSummary],[Disease]<disease%200..1-%20[DiseaseTreatmentSummary],[Disease])](https://yuml.me/diagram/nofunky;dir:TB/class/[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[Treatment],[Drug],[TreatmentAdverseEffect]<treatment_adverse_effects%200..*-++[DiseaseTreatmentSummary],[TreatmentEfficacy]<treatment_efficacies%200..*-++[DiseaseTreatmentSummary],[TreatmentMechanism]<treatment_mechanisms%200..*-++[DiseaseTreatmentSummary],[Treatment]<contraindications%200..*-%20[DiseaseTreatmentSummary],[Treatment]<treatments%200..*-%20[DiseaseTreatmentSummary],[Drug]<drugs%200..*-%20[DiseaseTreatmentSummary],[Disease]<disease%200..1-%20[DiseaseTreatmentSummary],[Disease]) - -## Attributes - - -### Own - - * [➞disease](diseaseTreatmentSummary__disease.md) <sub>0..1</sub> - * Description: the name of the disease that is treated. - * Range: [Disease](Disease.md) - * [➞drugs](diseaseTreatmentSummary__drugs.md) <sub>0..\*</sub> - * Description: semicolon-separated list of named small molecule drugs - * Range: [Drug](Drug.md) - * [➞treatments](diseaseTreatmentSummary__treatments.md) <sub>0..\*</sub> - * Description: semicolon-separated list of therapies and treatments are indicated for treating the disease. - * Range: [Treatment](Treatment.md) - * [➞contraindications](diseaseTreatmentSummary__contraindications.md) <sub>0..\*</sub> - * Description: semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects. - * Range: [Treatment](Treatment.md) - * [➞treatment_mechanisms](diseaseTreatmentSummary__treatment_mechanisms.md) <sub>0..\*</sub> - * Description: semicolon-separated list of treatment to asterisk-separated mechanism associations - * Range: [TreatmentMechanism](TreatmentMechanism.md) - * [➞treatment_efficacies](diseaseTreatmentSummary__treatment_efficacies.md) <sub>0..\*</sub> - * Description: semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective - * Range: [TreatmentEfficacy](TreatmentEfficacy.md) - * [➞treatment_adverse_effects](diseaseTreatmentSummary__treatment_adverse_effects.md) <sub>0..\*</sub> - * Description: semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea - * Range: [TreatmentAdverseEffect](TreatmentAdverseEffect.md) diff --git a/projects/treatment/docs/Drug.md b/projects/treatment/docs/Drug.md deleted file mode 100644 index 3bed19e60..000000000 --- a/projects/treatment/docs/Drug.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Drug - - - - -URI: [treatment:Drug](http://w3id.org/ontogpt/treatments/Drug) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiseaseTreatmentSummary]-%20drugs%200..*>[Drug|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Drug],[DiseaseTreatmentSummary])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[DiseaseTreatmentSummary]-%20drugs%200..*>[Drug|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Drug],[DiseaseTreatmentSummary]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞drugs](diseaseTreatmentSummary__drugs.md)* <sub>0..\*</sub> **[Drug](Drug.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/ExtractionResult.md b/projects/treatment/docs/ExtractionResult.md deleted file mode 100644 index 5a9073b6d..000000000 --- a/projects/treatment/docs/ExtractionResult.md +++ /dev/null @@ -1,32 +0,0 @@ - -# Class: ExtractionResult - - -A result of extracting knowledge on text - -URI: [treatment:ExtractionResult](http://w3id.org/ontogpt/treatments/ExtractionResult) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any])](https://yuml.me/diagram/nofunky;dir:TB/class/[Any]<named_entities%200..*-++[ExtractionResult|input_id:string%20%3F;input_title:string%20%3F;input_text:string%20%3F;raw_completion_output:string%20%3F;prompt:string%20%3F],[Any]<extracted_object%200..1-++[ExtractionResult],[Any]) - -## Attributes - - -### Own - - * [➞input_id](extractionResult__input_id.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_title](extractionResult__input_title.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞input_text](extractionResult__input_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞raw_completion_output](extractionResult__raw_completion_output.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞prompt](extractionResult__prompt.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞extracted_object](extractionResult__extracted_object.md) <sub>0..1</sub> - * Description: The complex objects extracted from the text - * Range: [Any](Any.md) - * [➞named_entities](extractionResult__named_entities.md) <sub>0..\*</sub> - * Description: Named entities extracted from the text - * Range: [Any](Any.md) diff --git a/projects/treatment/docs/Gene.md b/projects/treatment/docs/Gene.md deleted file mode 100644 index 25de630ea..000000000 --- a/projects/treatment/docs/Gene.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Gene - - - - -URI: [treatment:Gene](http://w3id.org/ontogpt/treatments/Gene) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[NamedEntity]^-[Gene|id(i):string;label(i):string%20%3F])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[NamedEntity]^-[Gene|id(i):string;label(i):string%20%3F]) - -## Identifier prefixes - - * HGNC - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/MAXOActionType.md b/projects/treatment/docs/MAXOActionType.md deleted file mode 100644 index 2b0fe096b..000000000 --- a/projects/treatment/docs/MAXOActionType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: MAXOActionType - - - - -URI: [treatment:MAXOActionType](http://w3id.org/ontogpt/treatments/MAXOActionType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/treatment/docs/MESHTherapeuticType.md b/projects/treatment/docs/MESHTherapeuticType.md deleted file mode 100644 index 0854fbe8a..000000000 --- a/projects/treatment/docs/MESHTherapeuticType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: MESHTherapeuticType - - - - -URI: [treatment:MESHTherapeuticType](http://w3id.org/ontogpt/treatments/MESHTherapeuticType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/treatment/docs/Mechanism.md b/projects/treatment/docs/Mechanism.md deleted file mode 100644 index 9f5b3b682..000000000 --- a/projects/treatment/docs/Mechanism.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Mechanism - - - - -URI: [treatment:Mechanism](http://w3id.org/ontogpt/treatments/Mechanism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[TreatmentMechanism]-%20mechanism%200..1>[Mechanism|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Mechanism],[TreatmentMechanism])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity],[TreatmentMechanism]-%20mechanism%200..1>[Mechanism|id(i):string;label(i):string%20%3F],[NamedEntity]^-[Mechanism],[TreatmentMechanism]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞mechanism](treatmentMechanism__mechanism.md)* <sub>0..1</sub> **[Mechanism](Mechanism.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/NCITDrugType.md b/projects/treatment/docs/NCITDrugType.md deleted file mode 100644 index 207ca34fc..000000000 --- a/projects/treatment/docs/NCITDrugType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: NCITDrugType - - - - -URI: [treatment:NCITDrugType](http://w3id.org/ontogpt/treatments/NCITDrugType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/treatment/docs/NCITTActivityType.md b/projects/treatment/docs/NCITTActivityType.md deleted file mode 100644 index 137a51225..000000000 --- a/projects/treatment/docs/NCITTActivityType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: NCITTActivityType - - - - -URI: [treatment:NCITTActivityType](http://w3id.org/ontogpt/treatments/NCITTActivityType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/treatment/docs/NCITTreatmentType.md b/projects/treatment/docs/NCITTreatmentType.md deleted file mode 100644 index 9c3f64e51..000000000 --- a/projects/treatment/docs/NCITTreatmentType.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Enum: NCITTreatmentType - - - - -URI: [treatment:NCITTreatmentType](http://w3id.org/ontogpt/treatments/NCITTreatmentType) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | - diff --git a/projects/treatment/docs/NamedEntity.md b/projects/treatment/docs/NamedEntity.md deleted file mode 100644 index 14298c0fa..000000000 --- a/projects/treatment/docs/NamedEntity.md +++ /dev/null @@ -1,40 +0,0 @@ - -# Class: NamedEntity - - - - -URI: [treatment:NamedEntity](http://w3id.org/ontogpt/treatments/NamedEntity) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Treatment],[Symptom],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Treatment],[NamedEntity]^-[Symptom],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Mechanism],[NamedEntity]^-[Gene],[NamedEntity]^-[Drug],[NamedEntity]^-[Disease],[NamedEntity]^-[AdverseEffect],[Triple],[Mechanism],[Gene],[Drug],[Disease],[AdverseEffect])](https://yuml.me/diagram/nofunky;dir:TB/class/[Treatment],[Symptom],[RelationshipType],[Triple]-%20object%200..1>[NamedEntity|id:string;label:string%20%3F],[Triple]-%20object_qualifier%200..1>[NamedEntity],[Triple]-%20subject%200..1>[NamedEntity],[Triple]-%20subject_qualifier%200..1>[NamedEntity],[NamedEntity]^-[Treatment],[NamedEntity]^-[Symptom],[NamedEntity]^-[RelationshipType],[NamedEntity]^-[Mechanism],[NamedEntity]^-[Gene],[NamedEntity]^-[Drug],[NamedEntity]^-[Disease],[NamedEntity]^-[AdverseEffect],[Triple],[Mechanism],[Gene],[Drug],[Disease],[AdverseEffect]) - -## Children - - * [AdverseEffect](AdverseEffect.md) - * [Disease](Disease.md) - * [Drug](Drug.md) - * [Gene](Gene.md) - * [Mechanism](Mechanism.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - * [Treatment](Treatment.md) - -## Referenced by Class - - * **None** *[➞object](triple__object.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞object_qualifier](triple__object_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject](triple__subject.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - * **None** *[➞subject_qualifier](triple__subject_qualifier.md)* <sub>0..1</sub> **[NamedEntity](NamedEntity.md)** - -## Attributes - - -### Own - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/NullDataOptions.md b/projects/treatment/docs/NullDataOptions.md deleted file mode 100644 index e1042633c..000000000 --- a/projects/treatment/docs/NullDataOptions.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Enum: NullDataOptions - - - - -URI: [treatment:NullDataOptions](http://w3id.org/ontogpt/treatments/NullDataOptions) - - -## Other properties - -| | | | -| --- | --- | --- | - -## Permissible Values - -| Text | Description | Meaning | Other Information | -| :--- | :---: | :---: | ---: | -| UNSPECIFIED_METHOD_OF_ADMINISTRATION | | NCIT:C149701 | | -| NOT_APPLICABLE | | NCIT:C18902 | {'aliases': ['not applicable', 'N/A']} | -| NOT_MENTIONED | | | | - diff --git a/projects/treatment/docs/Publication.md b/projects/treatment/docs/Publication.md deleted file mode 100644 index e32646674..000000000 --- a/projects/treatment/docs/Publication.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Publication - - - - -URI: [treatment:Publication](http://w3id.org/ontogpt/treatments/Publication) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples])](https://yuml.me/diagram/nofunky;dir:TB/class/[TextWithTriples]++-%20publication%200..1>[Publication|id:string%20%3F;title:string%20%3F;abstract:string%20%3F;combined_text:string%20%3F;full_text:string%20%3F],[TextWithTriples]) - -## Referenced by Class - - * **None** *[➞publication](textWithTriples__publication.md)* <sub>0..1</sub> **[Publication](Publication.md)** - -## Attributes - - -### Own - - * [➞id](publication__id.md) <sub>0..1</sub> - * Description: The publication identifier - * Range: [String](types/String.md) - * [➞title](publication__title.md) <sub>0..1</sub> - * Description: The title of the publication - * Range: [String](types/String.md) - * [➞abstract](publication__abstract.md) <sub>0..1</sub> - * Description: The abstract of the publication - * Range: [String](types/String.md) - * [➞combined_text](publication__combined_text.md) <sub>0..1</sub> - * Range: [String](types/String.md) - * [➞full_text](publication__full_text.md) <sub>0..1</sub> - * Description: The full text of the publication - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/RelationshipType.md b/projects/treatment/docs/RelationshipType.md deleted file mode 100644 index aa95855a1..000000000 --- a/projects/treatment/docs/RelationshipType.md +++ /dev/null @@ -1,35 +0,0 @@ - -# Class: RelationshipType - - - - -URI: [treatment:RelationshipType](http://w3id.org/ontogpt/treatments/RelationshipType) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple]-%20predicate%200..1>[RelationshipType|id(i):string;label(i):string%20%3F],[NamedEntity]^-[RelationshipType],[Triple],[NamedEntity]) - -## Identifier prefixes - - * RO - * biolink - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞predicate](triple__predicate.md)* <sub>0..1</sub> **[RelationshipType](RelationshipType.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/Symptom.md b/projects/treatment/docs/Symptom.md deleted file mode 100644 index 05d3d1aba..000000000 --- a/projects/treatment/docs/Symptom.md +++ /dev/null @@ -1,30 +0,0 @@ - -# Class: Symptom - - - - -URI: [treatment:Symptom](http://w3id.org/ontogpt/treatments/Symptom) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]^-[Symptom|id(i):string;label(i):string%20%3F],[NamedEntity])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]^-[Symptom|id(i):string;label(i):string%20%3F],[NamedEntity]) - -## Identifier prefixes - - * HP - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/TextWithTriples.md b/projects/treatment/docs/TextWithTriples.md deleted file mode 100644 index ac1a41b02..000000000 --- a/projects/treatment/docs/TextWithTriples.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Class: TextWithTriples - - - - -URI: [treatment:TextWithTriples](http://w3id.org/ontogpt/treatments/TextWithTriples) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication])](https://yuml.me/diagram/nofunky;dir:TB/class/[Triple],[Triple]<triples%200..*-++[TextWithTriples],[Publication]<publication%200..1-++[TextWithTriples],[Publication]) - -## Attributes - - -### Own - - * [➞publication](textWithTriples__publication.md) <sub>0..1</sub> - * Range: [Publication](Publication.md) - * [➞triples](textWithTriples__triples.md) <sub>0..\*</sub> - * Range: [Triple](Triple.md) diff --git a/projects/treatment/docs/TreatmentAdverseEffect.md b/projects/treatment/docs/TreatmentAdverseEffect.md deleted file mode 100644 index 566edd21d..000000000 --- a/projects/treatment/docs/TreatmentAdverseEffect.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: TreatmentAdverseEffect - - - - -URI: [treatment:TreatmentAdverseEffect](http://w3id.org/ontogpt/treatments/TreatmentAdverseEffect) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[AdverseEffect]<adverse_effects%200..*-%20[TreatmentAdverseEffect],[Treatment]<treatment%200..1-%20[TreatmentAdverseEffect],[DiseaseTreatmentSummary]++-%20treatment_adverse_effects%200..*>[TreatmentAdverseEffect],[CompoundExpression]^-[TreatmentAdverseEffect],[Treatment],[DiseaseTreatmentSummary],[CompoundExpression],[AdverseEffect])](https://yuml.me/diagram/nofunky;dir:TB/class/[AdverseEffect]<adverse_effects%200..*-%20[TreatmentAdverseEffect],[Treatment]<treatment%200..1-%20[TreatmentAdverseEffect],[DiseaseTreatmentSummary]++-%20treatment_adverse_effects%200..*>[TreatmentAdverseEffect],[CompoundExpression]^-[TreatmentAdverseEffect],[Treatment],[DiseaseTreatmentSummary],[CompoundExpression],[AdverseEffect]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞treatment_adverse_effects](diseaseTreatmentSummary__treatment_adverse_effects.md)* <sub>0..\*</sub> **[TreatmentAdverseEffect](TreatmentAdverseEffect.md)** - -## Attributes - - -### Own - - * [➞treatment](treatmentAdverseEffect__treatment.md) <sub>0..1</sub> - * Range: [Treatment](Treatment.md) - * [➞adverse_effects](treatmentAdverseEffect__adverse_effects.md) <sub>0..\*</sub> - * Range: [AdverseEffect](AdverseEffect.md) diff --git a/projects/treatment/docs/TreatmentEfficacy.md b/projects/treatment/docs/TreatmentEfficacy.md deleted file mode 100644 index f1e9c8c46..000000000 --- a/projects/treatment/docs/TreatmentEfficacy.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: TreatmentEfficacy - - - - -URI: [treatment:TreatmentEfficacy](http://w3id.org/ontogpt/treatments/TreatmentEfficacy) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Treatment]<treatment%200..1-%20[TreatmentEfficacy|efficacy:string%20%3F],[DiseaseTreatmentSummary]++-%20treatment_efficacies%200..*>[TreatmentEfficacy],[CompoundExpression]^-[TreatmentEfficacy],[Treatment],[DiseaseTreatmentSummary],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Treatment]<treatment%200..1-%20[TreatmentEfficacy|efficacy:string%20%3F],[DiseaseTreatmentSummary]++-%20treatment_efficacies%200..*>[TreatmentEfficacy],[CompoundExpression]^-[TreatmentEfficacy],[Treatment],[DiseaseTreatmentSummary],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞treatment_efficacies](diseaseTreatmentSummary__treatment_efficacies.md)* <sub>0..\*</sub> **[TreatmentEfficacy](TreatmentEfficacy.md)** - -## Attributes - - -### Own - - * [➞treatment](treatmentEfficacy__treatment.md) <sub>0..1</sub> - * Range: [Treatment](Treatment.md) - * [➞efficacy](treatmentEfficacy__efficacy.md) <sub>0..1</sub> - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/TreatmentMechanism.md b/projects/treatment/docs/TreatmentMechanism.md deleted file mode 100644 index f679702fc..000000000 --- a/projects/treatment/docs/TreatmentMechanism.md +++ /dev/null @@ -1,28 +0,0 @@ - -# Class: TreatmentMechanism - - - - -URI: [treatment:TreatmentMechanism](http://w3id.org/ontogpt/treatments/TreatmentMechanism) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[Mechanism]<mechanism%200..1-%20[TreatmentMechanism],[Treatment]<treatment%200..1-%20[TreatmentMechanism],[DiseaseTreatmentSummary]++-%20treatment_mechanisms%200..*>[TreatmentMechanism],[CompoundExpression]^-[TreatmentMechanism],[Treatment],[Mechanism],[DiseaseTreatmentSummary],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[Mechanism]<mechanism%200..1-%20[TreatmentMechanism],[Treatment]<treatment%200..1-%20[TreatmentMechanism],[DiseaseTreatmentSummary]++-%20treatment_mechanisms%200..*>[TreatmentMechanism],[CompoundExpression]^-[TreatmentMechanism],[Treatment],[Mechanism],[DiseaseTreatmentSummary],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞treatment_mechanisms](diseaseTreatmentSummary__treatment_mechanisms.md)* <sub>0..\*</sub> **[TreatmentMechanism](TreatmentMechanism.md)** - -## Attributes - - -### Own - - * [➞treatment](treatmentMechanism__treatment.md) <sub>0..1</sub> - * Range: [Treatment](Treatment.md) - * [➞mechanism](treatmentMechanism__mechanism.md) <sub>0..1</sub> - * Range: [Mechanism](Mechanism.md) diff --git a/projects/treatment/docs/Triple.md b/projects/treatment/docs/Triple.md deleted file mode 100644 index 758d9b45c..000000000 --- a/projects/treatment/docs/Triple.md +++ /dev/null @@ -1,39 +0,0 @@ - -# Class: Triple - - -Abstract parent for Relation Extraction tasks - -URI: [treatment:Triple](http://w3id.org/ontogpt/treatments/Triple) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression])](https://yuml.me/diagram/nofunky;dir:TB/class/[NamedEntity]<object_qualifier%200..1-%20[Triple|qualifier:string%20%3F],[NamedEntity]<subject_qualifier%200..1-%20[Triple],[NamedEntity]<object%200..1-%20[Triple],[RelationshipType]<predicate%200..1-%20[Triple],[NamedEntity]<subject%200..1-%20[Triple],[TextWithTriples]++-%20triples%200..*>[Triple],[CompoundExpression]^-[Triple],[TextWithTriples],[RelationshipType],[NamedEntity],[CompoundExpression]) - -## Parents - - * is_a: [CompoundExpression](CompoundExpression.md) - -## Referenced by Class - - * **None** *[➞triples](textWithTriples__triples.md)* <sub>0..\*</sub> **[Triple](Triple.md)** - -## Attributes - - -### Own - - * [➞subject](triple__subject.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞predicate](triple__predicate.md) <sub>0..1</sub> - * Range: [RelationshipType](RelationshipType.md) - * [➞object](triple__object.md) <sub>0..1</sub> - * Range: [NamedEntity](NamedEntity.md) - * [➞qualifier](triple__qualifier.md) <sub>0..1</sub> - * Description: A qualifier for the statements, e.g. "NOT" for negation - * Range: [String](types/String.md) - * [➞subject_qualifier](triple__subject_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - * Range: [NamedEntity](NamedEntity.md) - * [➞object_qualifier](triple__object_qualifier.md) <sub>0..1</sub> - * Description: An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - * Range: [NamedEntity](NamedEntity.md) diff --git a/projects/treatment/docs/annotatorResult__object_id.md b/projects/treatment/docs/annotatorResult__object_id.md deleted file mode 100644 index 02bcff799..000000000 --- a/projects/treatment/docs/annotatorResult__object_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_id - - - - -URI: [treatment:annotatorResult__object_id](http://w3id.org/ontogpt/treatments/annotatorResult__object_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/treatment/docs/annotatorResult__object_text.md b/projects/treatment/docs/annotatorResult__object_text.md deleted file mode 100644 index a318994e9..000000000 --- a/projects/treatment/docs/annotatorResult__object_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_text - - - - -URI: [treatment:annotatorResult__object_text](http://w3id.org/ontogpt/treatments/annotatorResult__object_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/treatment/docs/annotatorResult__subject_text.md b/projects/treatment/docs/annotatorResult__subject_text.md deleted file mode 100644 index b04025e26..000000000 --- a/projects/treatment/docs/annotatorResult__subject_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_text - - - - -URI: [treatment:annotatorResult__subject_text](http://w3id.org/ontogpt/treatments/annotatorResult__subject_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AnnotatorResult](AnnotatorResult.md) diff --git a/projects/treatment/docs/diseaseTreatmentSummary__contraindications.md b/projects/treatment/docs/diseaseTreatmentSummary__contraindications.md deleted file mode 100644 index 4c67b2b00..000000000 --- a/projects/treatment/docs/diseaseTreatmentSummary__contraindications.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: contraindications - - -semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects. - -URI: [treatment:diseaseTreatmentSummary__contraindications](http://w3id.org/ontogpt/treatments/diseaseTreatmentSummary__contraindications) - - -## Domain and Range - -None → <sub>0..\*</sub> [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseTreatmentSummary](DiseaseTreatmentSummary.md) diff --git a/projects/treatment/docs/diseaseTreatmentSummary__disease.md b/projects/treatment/docs/diseaseTreatmentSummary__disease.md deleted file mode 100644 index c5fb326eb..000000000 --- a/projects/treatment/docs/diseaseTreatmentSummary__disease.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: disease - - -the name of the disease that is treated. - -URI: [treatment:diseaseTreatmentSummary__disease](http://w3id.org/ontogpt/treatments/diseaseTreatmentSummary__disease) - - -## Domain and Range - -None → <sub>0..1</sub> [Disease](Disease.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseTreatmentSummary](DiseaseTreatmentSummary.md) diff --git a/projects/treatment/docs/diseaseTreatmentSummary__drugs.md b/projects/treatment/docs/diseaseTreatmentSummary__drugs.md deleted file mode 100644 index a7e766a23..000000000 --- a/projects/treatment/docs/diseaseTreatmentSummary__drugs.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: drugs - - -semicolon-separated list of named small molecule drugs - -URI: [treatment:diseaseTreatmentSummary__drugs](http://w3id.org/ontogpt/treatments/diseaseTreatmentSummary__drugs) - - -## Domain and Range - -None → <sub>0..\*</sub> [Drug](Drug.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseTreatmentSummary](DiseaseTreatmentSummary.md) diff --git a/projects/treatment/docs/diseaseTreatmentSummary__treatment_adverse_effects.md b/projects/treatment/docs/diseaseTreatmentSummary__treatment_adverse_effects.md deleted file mode 100644 index 1171a5eb4..000000000 --- a/projects/treatment/docs/diseaseTreatmentSummary__treatment_adverse_effects.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment_adverse_effects - - -semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea - -URI: [treatment:diseaseTreatmentSummary__treatment_adverse_effects](http://w3id.org/ontogpt/treatments/diseaseTreatmentSummary__treatment_adverse_effects) - - -## Domain and Range - -None → <sub>0..\*</sub> [TreatmentAdverseEffect](TreatmentAdverseEffect.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseTreatmentSummary](DiseaseTreatmentSummary.md) diff --git a/projects/treatment/docs/diseaseTreatmentSummary__treatment_efficacies.md b/projects/treatment/docs/diseaseTreatmentSummary__treatment_efficacies.md deleted file mode 100644 index 9da50e227..000000000 --- a/projects/treatment/docs/diseaseTreatmentSummary__treatment_efficacies.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment_efficacies - - -semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective - -URI: [treatment:diseaseTreatmentSummary__treatment_efficacies](http://w3id.org/ontogpt/treatments/diseaseTreatmentSummary__treatment_efficacies) - - -## Domain and Range - -None → <sub>0..\*</sub> [TreatmentEfficacy](TreatmentEfficacy.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseTreatmentSummary](DiseaseTreatmentSummary.md) diff --git a/projects/treatment/docs/diseaseTreatmentSummary__treatment_mechanisms.md b/projects/treatment/docs/diseaseTreatmentSummary__treatment_mechanisms.md deleted file mode 100644 index 4e152c17d..000000000 --- a/projects/treatment/docs/diseaseTreatmentSummary__treatment_mechanisms.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment_mechanisms - - -semicolon-separated list of treatment to asterisk-separated mechanism associations - -URI: [treatment:diseaseTreatmentSummary__treatment_mechanisms](http://w3id.org/ontogpt/treatments/diseaseTreatmentSummary__treatment_mechanisms) - - -## Domain and Range - -None → <sub>0..\*</sub> [TreatmentMechanism](TreatmentMechanism.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseTreatmentSummary](DiseaseTreatmentSummary.md) diff --git a/projects/treatment/docs/diseaseTreatmentSummary__treatments.md b/projects/treatment/docs/diseaseTreatmentSummary__treatments.md deleted file mode 100644 index ec1002dfb..000000000 --- a/projects/treatment/docs/diseaseTreatmentSummary__treatments.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatments - - -semicolon-separated list of therapies and treatments are indicated for treating the disease. - -URI: [treatment:diseaseTreatmentSummary__treatments](http://w3id.org/ontogpt/treatments/diseaseTreatmentSummary__treatments) - - -## Domain and Range - -None → <sub>0..\*</sub> [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [DiseaseTreatmentSummary](DiseaseTreatmentSummary.md) diff --git a/projects/treatment/docs/extractionResult__extracted_object.md b/projects/treatment/docs/extractionResult__extracted_object.md deleted file mode 100644 index 455833d35..000000000 --- a/projects/treatment/docs/extractionResult__extracted_object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: extracted_object - - -The complex objects extracted from the text - -URI: [treatment:extractionResult__extracted_object](http://w3id.org/ontogpt/treatments/extractionResult__extracted_object) - - -## Domain and Range - -None → <sub>0..1</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/treatment/docs/extractionResult__input_id.md b/projects/treatment/docs/extractionResult__input_id.md deleted file mode 100644 index 31fd80560..000000000 --- a/projects/treatment/docs/extractionResult__input_id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_id - - - - -URI: [treatment:extractionResult__input_id](http://w3id.org/ontogpt/treatments/extractionResult__input_id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/treatment/docs/extractionResult__input_text.md b/projects/treatment/docs/extractionResult__input_text.md deleted file mode 100644 index 50cc4f58e..000000000 --- a/projects/treatment/docs/extractionResult__input_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_text - - - - -URI: [treatment:extractionResult__input_text](http://w3id.org/ontogpt/treatments/extractionResult__input_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/treatment/docs/extractionResult__input_title.md b/projects/treatment/docs/extractionResult__input_title.md deleted file mode 100644 index c2c211e2e..000000000 --- a/projects/treatment/docs/extractionResult__input_title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: input_title - - - - -URI: [treatment:extractionResult__input_title](http://w3id.org/ontogpt/treatments/extractionResult__input_title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/treatment/docs/extractionResult__named_entities.md b/projects/treatment/docs/extractionResult__named_entities.md deleted file mode 100644 index 7394e2a73..000000000 --- a/projects/treatment/docs/extractionResult__named_entities.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: named_entities - - -Named entities extracted from the text - -URI: [treatment:extractionResult__named_entities](http://w3id.org/ontogpt/treatments/extractionResult__named_entities) - - -## Domain and Range - -None → <sub>0..\*</sub> [Any](Any.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/treatment/docs/extractionResult__prompt.md b/projects/treatment/docs/extractionResult__prompt.md deleted file mode 100644 index 6212791e0..000000000 --- a/projects/treatment/docs/extractionResult__prompt.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: prompt - - - - -URI: [treatment:extractionResult__prompt](http://w3id.org/ontogpt/treatments/extractionResult__prompt) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/treatment/docs/extractionResult__raw_completion_output.md b/projects/treatment/docs/extractionResult__raw_completion_output.md deleted file mode 100644 index 2948d0656..000000000 --- a/projects/treatment/docs/extractionResult__raw_completion_output.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: raw_completion_output - - - - -URI: [treatment:extractionResult__raw_completion_output](http://w3id.org/ontogpt/treatments/extractionResult__raw_completion_output) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [ExtractionResult](ExtractionResult.md) diff --git a/projects/treatment/docs/namedEntity__id.md b/projects/treatment/docs/namedEntity__id.md deleted file mode 100644 index d15dd9322..000000000 --- a/projects/treatment/docs/namedEntity__id.md +++ /dev/null @@ -1,37 +0,0 @@ - -# Slot: id - - -A unique identifier for the named entity - -URI: [treatment:namedEntity__id](http://w3id.org/ontogpt/treatments/namedEntity__id) - - -## Domain and Range - -None → <sub>1..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AdverseEffect](AdverseEffect.md) - * [Disease](Disease.md) - * [Drug](Drug.md) - * [Gene](Gene.md) - * [Mechanism](Mechanism.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - * [Treatment](Treatment.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | this is populated during the grounding and normalization step | - diff --git a/projects/treatment/docs/namedEntity__label.md b/projects/treatment/docs/namedEntity__label.md deleted file mode 100644 index 2cb998313..000000000 --- a/projects/treatment/docs/namedEntity__label.md +++ /dev/null @@ -1,38 +0,0 @@ - -# Slot: label - - -The label (name) of the named thing - -URI: [treatment:namedEntity__label](http://w3id.org/ontogpt/treatments/namedEntity__label) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [AdverseEffect](AdverseEffect.md) - * [Disease](Disease.md) - * [Drug](Drug.md) - * [Gene](Gene.md) - * [Mechanism](Mechanism.md) - * [NamedEntity](NamedEntity.md) - * [RelationshipType](RelationshipType.md) - * [Symptom](Symptom.md) - * [Treatment](Treatment.md) - -## Other properties - -| | | | -| --- | --- | --- | -| **Aliases:** | | name | -| **Mappings:** | | rdfs:label | - diff --git a/projects/treatment/docs/publication__abstract.md b/projects/treatment/docs/publication__abstract.md deleted file mode 100644 index f406354ef..000000000 --- a/projects/treatment/docs/publication__abstract.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: abstract - - -The abstract of the publication - -URI: [treatment:publication__abstract](http://w3id.org/ontogpt/treatments/publication__abstract) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/treatment/docs/publication__combined_text.md b/projects/treatment/docs/publication__combined_text.md deleted file mode 100644 index 6d29fcece..000000000 --- a/projects/treatment/docs/publication__combined_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: combined_text - - - - -URI: [treatment:publication__combined_text](http://w3id.org/ontogpt/treatments/publication__combined_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/treatment/docs/publication__full_text.md b/projects/treatment/docs/publication__full_text.md deleted file mode 100644 index 5761cb8f8..000000000 --- a/projects/treatment/docs/publication__full_text.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: full_text - - -The full text of the publication - -URI: [treatment:publication__full_text](http://w3id.org/ontogpt/treatments/publication__full_text) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/treatment/docs/publication__id.md b/projects/treatment/docs/publication__id.md deleted file mode 100644 index 8f426fe8a..000000000 --- a/projects/treatment/docs/publication__id.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: id - - -The publication identifier - -URI: [treatment:publication__id](http://w3id.org/ontogpt/treatments/publication__id) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/treatment/docs/publication__title.md b/projects/treatment/docs/publication__title.md deleted file mode 100644 index 562b800b5..000000000 --- a/projects/treatment/docs/publication__title.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: title - - -The title of the publication - -URI: [treatment:publication__title](http://w3id.org/ontogpt/treatments/publication__title) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Publication](Publication.md) diff --git a/projects/treatment/docs/textWithTriples__publication.md b/projects/treatment/docs/textWithTriples__publication.md deleted file mode 100644 index c30861d98..000000000 --- a/projects/treatment/docs/textWithTriples__publication.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: publication - - - - -URI: [treatment:textWithTriples__publication](http://w3id.org/ontogpt/treatments/textWithTriples__publication) - - -## Domain and Range - -None → <sub>0..1</sub> [Publication](Publication.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/treatment/docs/textWithTriples__triples.md b/projects/treatment/docs/textWithTriples__triples.md deleted file mode 100644 index 95ed30315..000000000 --- a/projects/treatment/docs/textWithTriples__triples.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: triples - - - - -URI: [treatment:textWithTriples__triples](http://w3id.org/ontogpt/treatments/textWithTriples__triples) - - -## Domain and Range - -None → <sub>0..\*</sub> [Triple](Triple.md) - -## Parents - - -## Children - - -## Used by - - * [TextWithTriples](TextWithTriples.md) diff --git a/projects/treatment/docs/treatment.md b/projects/treatment/docs/treatment.md deleted file mode 100644 index 97abd9181..000000000 --- a/projects/treatment/docs/treatment.md +++ /dev/null @@ -1,34 +0,0 @@ - -# Class: Treatment - - - - -URI: [treatment:Treatment](http://w3id.org/ontogpt/treatments/Treatment) - - -[![img](https://yuml.me/diagram/nofunky;dir:TB/class/[DiseaseTreatmentSummary]-%20contraindications%200..*>[Treatment|id(i):string;label(i):string%20%3F],[DiseaseTreatmentSummary]-%20treatments%200..*>[Treatment],[TreatmentAdverseEffect]-%20treatment%200..1>[Treatment],[TreatmentEfficacy]-%20treatment%200..1>[Treatment],[TreatmentMechanism]-%20treatment%200..1>[Treatment],[NamedEntity]^-[Treatment],[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[NamedEntity],[DiseaseTreatmentSummary])](https://yuml.me/diagram/nofunky;dir:TB/class/[DiseaseTreatmentSummary]-%20contraindications%200..*>[Treatment|id(i):string;label(i):string%20%3F],[DiseaseTreatmentSummary]-%20treatments%200..*>[Treatment],[TreatmentAdverseEffect]-%20treatment%200..1>[Treatment],[TreatmentEfficacy]-%20treatment%200..1>[Treatment],[TreatmentMechanism]-%20treatment%200..1>[Treatment],[NamedEntity]^-[Treatment],[TreatmentMechanism],[TreatmentEfficacy],[TreatmentAdverseEffect],[NamedEntity],[DiseaseTreatmentSummary]) - -## Parents - - * is_a: [NamedEntity](NamedEntity.md) - -## Referenced by Class - - * **None** *[➞contraindications](diseaseTreatmentSummary__contraindications.md)* <sub>0..\*</sub> **[Treatment](Treatment.md)** - * **None** *[➞treatments](diseaseTreatmentSummary__treatments.md)* <sub>0..\*</sub> **[Treatment](Treatment.md)** - * **None** *[➞treatment](treatmentAdverseEffect__treatment.md)* <sub>0..1</sub> **[Treatment](Treatment.md)** - * **None** *[➞treatment](treatmentEfficacy__treatment.md)* <sub>0..1</sub> **[Treatment](Treatment.md)** - * **None** *[➞treatment](treatmentMechanism__treatment.md)* <sub>0..1</sub> **[Treatment](Treatment.md)** - -## Attributes - - -### Inherited from NamedEntity: - - * [➞id](namedEntity__id.md) <sub>1..1</sub> - * Description: A unique identifier for the named entity - * Range: [String](types/String.md) - * [➞label](namedEntity__label.md) <sub>0..1</sub> - * Description: The label (name) of the named thing - * Range: [String](types/String.md) diff --git a/projects/treatment/docs/treatmentAdverseEffect__adverse_effects.md b/projects/treatment/docs/treatmentAdverseEffect__adverse_effects.md deleted file mode 100644 index 63a57698c..000000000 --- a/projects/treatment/docs/treatmentAdverseEffect__adverse_effects.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: adverse_effects - - - - -URI: [treatment:treatmentAdverseEffect__adverse_effects](http://w3id.org/ontogpt/treatments/treatmentAdverseEffect__adverse_effects) - - -## Domain and Range - -None → <sub>0..\*</sub> [AdverseEffect](AdverseEffect.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentAdverseEffect](TreatmentAdverseEffect.md) diff --git a/projects/treatment/docs/treatmentAdverseEffect__treatment.md b/projects/treatment/docs/treatmentAdverseEffect__treatment.md deleted file mode 100644 index 5f377383a..000000000 --- a/projects/treatment/docs/treatmentAdverseEffect__treatment.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment - - - - -URI: [treatment:treatmentAdverseEffect__treatment](http://w3id.org/ontogpt/treatments/treatmentAdverseEffect__treatment) - - -## Domain and Range - -None → <sub>0..1</sub> [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentAdverseEffect](TreatmentAdverseEffect.md) diff --git a/projects/treatment/docs/treatmentEfficacy__efficacy.md b/projects/treatment/docs/treatmentEfficacy__efficacy.md deleted file mode 100644 index 51f902c15..000000000 --- a/projects/treatment/docs/treatmentEfficacy__efficacy.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: efficacy - - - - -URI: [treatment:treatmentEfficacy__efficacy](http://w3id.org/ontogpt/treatments/treatmentEfficacy__efficacy) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentEfficacy](TreatmentEfficacy.md) diff --git a/projects/treatment/docs/treatmentEfficacy__treatment.md b/projects/treatment/docs/treatmentEfficacy__treatment.md deleted file mode 100644 index fab6d5f8f..000000000 --- a/projects/treatment/docs/treatmentEfficacy__treatment.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment - - - - -URI: [treatment:treatmentEfficacy__treatment](http://w3id.org/ontogpt/treatments/treatmentEfficacy__treatment) - - -## Domain and Range - -None → <sub>0..1</sub> [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentEfficacy](TreatmentEfficacy.md) diff --git a/projects/treatment/docs/treatmentMechanism__mechanism.md b/projects/treatment/docs/treatmentMechanism__mechanism.md deleted file mode 100644 index bd063cfbe..000000000 --- a/projects/treatment/docs/treatmentMechanism__mechanism.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: mechanism - - - - -URI: [treatment:treatmentMechanism__mechanism](http://w3id.org/ontogpt/treatments/treatmentMechanism__mechanism) - - -## Domain and Range - -None → <sub>0..1</sub> [Mechanism](Mechanism.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentMechanism](TreatmentMechanism.md) diff --git a/projects/treatment/docs/treatmentMechanism__treatment.md b/projects/treatment/docs/treatmentMechanism__treatment.md deleted file mode 100644 index b721b4cd8..000000000 --- a/projects/treatment/docs/treatmentMechanism__treatment.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: treatment - - - - -URI: [treatment:treatmentMechanism__treatment](http://w3id.org/ontogpt/treatments/treatmentMechanism__treatment) - - -## Domain and Range - -None → <sub>0..1</sub> [Treatment](Treatment.md) - -## Parents - - -## Children - - -## Used by - - * [TreatmentMechanism](TreatmentMechanism.md) diff --git a/projects/treatment/docs/triple__object.md b/projects/treatment/docs/triple__object.md deleted file mode 100644 index ad7e70bd2..000000000 --- a/projects/treatment/docs/triple__object.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object - - - - -URI: [treatment:triple__object](http://w3id.org/ontogpt/treatments/triple__object) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/treatment/docs/triple__object_qualifier.md b/projects/treatment/docs/triple__object_qualifier.md deleted file mode 100644 index a649d636d..000000000 --- a/projects/treatment/docs/triple__object_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: object_qualifier - - -An optional qualifier or modifier for the object of the statement, e.g. "severe" or "with additional complications" - -URI: [treatment:triple__object_qualifier](http://w3id.org/ontogpt/treatments/triple__object_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/treatment/docs/triple__predicate.md b/projects/treatment/docs/triple__predicate.md deleted file mode 100644 index 6d05e896f..000000000 --- a/projects/treatment/docs/triple__predicate.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: predicate - - - - -URI: [treatment:triple__predicate](http://w3id.org/ontogpt/treatments/triple__predicate) - - -## Domain and Range - -None → <sub>0..1</sub> [RelationshipType](RelationshipType.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/treatment/docs/triple__qualifier.md b/projects/treatment/docs/triple__qualifier.md deleted file mode 100644 index bdc6c1e95..000000000 --- a/projects/treatment/docs/triple__qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: qualifier - - -A qualifier for the statements, e.g. "NOT" for negation - -URI: [treatment:triple__qualifier](http://w3id.org/ontogpt/treatments/triple__qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [String](types/String.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/treatment/docs/triple__subject.md b/projects/treatment/docs/triple__subject.md deleted file mode 100644 index 6675a6fab..000000000 --- a/projects/treatment/docs/triple__subject.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject - - - - -URI: [treatment:triple__subject](http://w3id.org/ontogpt/treatments/triple__subject) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/treatment/docs/triple__subject_qualifier.md b/projects/treatment/docs/triple__subject_qualifier.md deleted file mode 100644 index ec2f79e2d..000000000 --- a/projects/treatment/docs/triple__subject_qualifier.md +++ /dev/null @@ -1,22 +0,0 @@ - -# Slot: subject_qualifier - - -An optional qualifier or modifier for the subject of the statement, e.g. "high dose" or "intravenously administered" - -URI: [treatment:triple__subject_qualifier](http://w3id.org/ontogpt/treatments/triple__subject_qualifier) - - -## Domain and Range - -None → <sub>0..1</sub> [NamedEntity](NamedEntity.md) - -## Parents - - -## Children - - -## Used by - - * [Triple](Triple.md) diff --git a/projects/treatment/docs/types/Boolean.md b/projects/treatment/docs/types/Boolean.md deleted file mode 100644 index dc83a9c6e..000000000 --- a/projects/treatment/docs/types/Boolean.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: boolean - - -A binary (true or false) value - -URI: [linkml:Boolean](https://w3id.org/linkml/Boolean) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Bool** | -| Representation | | bool | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Boolean | - diff --git a/projects/treatment/docs/types/Curie.md b/projects/treatment/docs/types/Curie.md deleted file mode 100644 index c1803f93f..000000000 --- a/projects/treatment/docs/types/Curie.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: curie - - -a compact URI - -URI: [linkml:Curie](https://w3id.org/linkml/Curie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Curie** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations this MUST be expanded to a URI | -| | | in non-RDF serializations MAY be serialized as the compact representation | - diff --git a/projects/treatment/docs/types/Date.md b/projects/treatment/docs/types/Date.md deleted file mode 100644 index 06948af97..000000000 --- a/projects/treatment/docs/types/Date.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: date - - -a date (year, month and day) in an idealized calendar - -URI: [linkml:Date](https://w3id.org/linkml/Date) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDate** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Date | - diff --git a/projects/treatment/docs/types/DateOrDatetime.md b/projects/treatment/docs/types/DateOrDatetime.md deleted file mode 100644 index ef983898d..000000000 --- a/projects/treatment/docs/types/DateOrDatetime.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: date_or_datetime - - -Either a date or a datetime - -URI: [linkml:DateOrDatetime](https://w3id.org/linkml/DateOrDatetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/treatment/docs/types/Datetime.md b/projects/treatment/docs/types/Datetime.md deleted file mode 100644 index 9510454a8..000000000 --- a/projects/treatment/docs/types/Datetime.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: datetime - - -The combination of a date and time - -URI: [linkml:Datetime](https://w3id.org/linkml/Datetime) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDDateTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:DateTime | - diff --git a/projects/treatment/docs/types/Decimal.md b/projects/treatment/docs/types/Decimal.md deleted file mode 100644 index a7ba14a5d..000000000 --- a/projects/treatment/docs/types/Decimal.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: decimal - - -A real number with arbitrary precision that conforms to the xsd:decimal specification - -URI: [linkml:Decimal](https://w3id.org/linkml/Decimal) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **Decimal** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Broad Mappings:** | | schema:Number | - diff --git a/projects/treatment/docs/types/Double.md b/projects/treatment/docs/types/Double.md deleted file mode 100644 index cfe6d71e2..000000000 --- a/projects/treatment/docs/types/Double.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: double - - -A real number that conforms to the xsd:double specification - -URI: [linkml:Double](https://w3id.org/linkml/Double) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Close Mappings:** | | schema:Float | - diff --git a/projects/treatment/docs/types/Float.md b/projects/treatment/docs/types/Float.md deleted file mode 100644 index 7b303f96f..000000000 --- a/projects/treatment/docs/types/Float.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: float - - -A real number that conforms to the xsd:float specification - -URI: [linkml:Float](https://w3id.org/linkml/Float) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **float** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Float | - diff --git a/projects/treatment/docs/types/Integer.md b/projects/treatment/docs/types/Integer.md deleted file mode 100644 index 3cfcc66d9..000000000 --- a/projects/treatment/docs/types/Integer.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: integer - - -An integer - -URI: [linkml:Integer](https://w3id.org/linkml/Integer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **int** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Integer | - diff --git a/projects/treatment/docs/types/Jsonpath.md b/projects/treatment/docs/types/Jsonpath.md deleted file mode 100644 index a03a58e67..000000000 --- a/projects/treatment/docs/types/Jsonpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpath - - -A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpath](https://w3id.org/linkml/Jsonpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/treatment/docs/types/Jsonpointer.md b/projects/treatment/docs/types/Jsonpointer.md deleted file mode 100644 index a0e1ac492..000000000 --- a/projects/treatment/docs/types/Jsonpointer.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: jsonpointer - - -A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. - -URI: [linkml:Jsonpointer](https://w3id.org/linkml/Jsonpointer) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/treatment/docs/types/Ncname.md b/projects/treatment/docs/types/Ncname.md deleted file mode 100644 index 710b0b04a..000000000 --- a/projects/treatment/docs/types/Ncname.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: ncname - - -Prefix part of CURIE - -URI: [linkml:Ncname](https://w3id.org/linkml/Ncname) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NCName** | -| Representation | | str | diff --git a/projects/treatment/docs/types/Nodeidentifier.md b/projects/treatment/docs/types/Nodeidentifier.md deleted file mode 100644 index f0097cdf4..000000000 --- a/projects/treatment/docs/types/Nodeidentifier.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: nodeidentifier - - -A URI, CURIE or BNODE that represents a node in a model. - -URI: [linkml:Nodeidentifier](https://w3id.org/linkml/Nodeidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **NodeIdentifier** | -| Representation | | str | diff --git a/projects/treatment/docs/types/Objectidentifier.md b/projects/treatment/docs/types/Objectidentifier.md deleted file mode 100644 index 454ba6be6..000000000 --- a/projects/treatment/docs/types/Objectidentifier.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: objectidentifier - - -A URI or CURIE that represents an object in the model. - -URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **ElementIdentifier** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | Used for inheritance and type checking | - diff --git a/projects/treatment/docs/types/Sparqlpath.md b/projects/treatment/docs/types/Sparqlpath.md deleted file mode 100644 index fd99a927e..000000000 --- a/projects/treatment/docs/types/Sparqlpath.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: sparqlpath - - -A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. - -URI: [linkml:Sparqlpath](https://w3id.org/linkml/Sparqlpath) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | -| Representation | | str | diff --git a/projects/treatment/docs/types/String.md b/projects/treatment/docs/types/String.md deleted file mode 100644 index 6e61d7081..000000000 --- a/projects/treatment/docs/types/String.md +++ /dev/null @@ -1,18 +0,0 @@ - -# Type: string - - -A character string - -URI: [linkml:String](https://w3id.org/linkml/String) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **str** | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Text | - diff --git a/projects/treatment/docs/types/Time.md b/projects/treatment/docs/types/Time.md deleted file mode 100644 index 2b8652bcd..000000000 --- a/projects/treatment/docs/types/Time.md +++ /dev/null @@ -1,19 +0,0 @@ - -# Type: time - - -A time object represents a (local) time of day, independent of any particular day - -URI: [linkml:Time](https://w3id.org/linkml/Time) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **XSDTime** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Exact Mappings:** | | schema:Time | - diff --git a/projects/treatment/docs/types/Uri.md b/projects/treatment/docs/types/Uri.md deleted file mode 100644 index 343807a5e..000000000 --- a/projects/treatment/docs/types/Uri.md +++ /dev/null @@ -1,20 +0,0 @@ - -# Type: uri - - -a complete URI - -URI: [linkml:Uri](https://w3id.org/linkml/Uri) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URI** | -| Representation | | str | - -## Other properties - -| | | | -| --- | --- | --- | -| **Comments:** | | in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node | -| **Close Mappings:** | | schema:URL | - diff --git a/projects/treatment/docs/types/Uriorcurie.md b/projects/treatment/docs/types/Uriorcurie.md deleted file mode 100644 index 2f7b65087..000000000 --- a/projects/treatment/docs/types/Uriorcurie.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Type: uriorcurie - - -a URI or a CURIE - -URI: [linkml:Uriorcurie](https://w3id.org/linkml/Uriorcurie) - -| | | | -| --- | --- | --- | -| Root (builtin) type | | **URIorCURIE** | -| Representation | | str | diff --git a/projects/treatment/excel/treatment.xlsx b/projects/treatment/excel/treatment.xlsx deleted file mode 100644 index 733b783180871a681a92ee1651e489869d11fe9a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 12566 zcmeHtWmH_-(rx1o!4sUI!QGwU!QDO31cx9A4#8a$oM6F8aCdhJuE8y6aCr^6_vD1j zx$pe>#{F}8jNMI-!J55xRn1*hbCsMF1SAFk0DuKNR)tX&)o4QW0)6`ox*mZpBP&BW 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cc70eff10..000000000 --- a/projects/treatment/graphql/treatment.graphql +++ /dev/null @@ -1,134 +0,0 @@ -type AdverseEffect - { - id: String! - label: String - } - -type AnnotatorResult - { - subjectText: String - objectId: String - objectText: String - } - -type Any - { - } - -interface CompoundExpression - { - } - -type Disease - { - id: String! - label: String - } - -type DiseaseTreatmentSummary - { - disease: Disease - drugs: [Drug] - treatments: [Treatment] - contraindications: [Treatment] - treatmentMechanisms: [TreatmentMechanism] - treatmentEfficacies: [TreatmentEfficacy] - treatmentAdverseEffects: [TreatmentAdverseEffect] - } - -type Drug - { - id: String! - label: String - } - -type ExtractionResult - { - inputId: String - inputTitle: String - inputText: String - rawCompletionOutput: String - prompt: String - extractedObject: Any - namedEntities: [Any] - } - -type Gene - { - id: String! - label: String - } - -type Mechanism - { - id: String! - label: String - } - -interface NamedEntity - { - id: String! - label: String - } - -type Publication - { - id: String - title: String - abstract: String - combinedText: String - fullText: String - } - -type RelationshipType - { - id: String! - label: String - } - -type Symptom - { - id: String! - label: String - } - -type TextWithTriples - { - publication: Publication - triples: [Triple] - } - -type Treatment - { - id: String! - label: String - } - -type TreatmentAdverseEffect - { - treatment: Treatment - adverseEffects: [AdverseEffect] - } - -type TreatmentEfficacy - { - treatment: Treatment - efficacy: String - } - -type TreatmentMechanism - { - treatment: Treatment - mechanism: Mechanism - } - -interface Triple - { - subject: NamedEntity - predicate: RelationshipType - object: NamedEntity - qualifier: String - subjectQualifier: NamedEntity - objectQualifier: NamedEntity - } - diff --git a/projects/treatment/jsonld/treatment.context.jsonld b/projects/treatment/jsonld/treatment.context.jsonld deleted file mode 100644 index b71dfde88..000000000 --- a/projects/treatment/jsonld/treatment.context.jsonld +++ /dev/null @@ -1,158 +0,0 @@ -{ - "comments": { - "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2023-08-07T10:56:36", - "source": "treatment.yaml" - }, - "@context": { - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "HP": "http://example.org/UNKNOWN/HP/", - "RO": { - "@id": "http://purl.obolibrary.org/obo/RO_", - "@prefix": true - }, - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "treatment": { - "@type": "@id" - }, - "@vocab": "http://w3id.org/ontogpt/treatments/", - "object_id": { - "@id": "core:object_id" - }, - "object_text": { - "@id": "core:object_text" - }, - "subject_text": { - "@id": "core:subject_text" - }, - "contraindications": { - "@type": "@id" - }, - "disease": { - "@type": "@id" - }, - "drugs": { - "@type": "@id" - }, - "treatment_adverse_effects": { - "@type": "@id" - }, - "treatment_efficacies": { - "@type": "@id" - }, - "treatment_mechanisms": { - "@type": "@id" - }, - "treatments": { - "@type": "@id" - }, - "extracted_object": { - "@type": "@id", - "@id": "core:extracted_object" - }, - "input_id": { - "@id": "core:input_id" - }, - "input_text": { - "@id": "core:input_text" - }, - "input_title": { - "@id": "core:input_title" - }, - "named_entities": { - "@type": "@id", - "@id": "core:named_entities" - }, - "prompt": { - "@id": "core:prompt" - }, - "raw_completion_output": { - "@id": "core:raw_completion_output" - }, - "id": { - "@id": "core:id" - }, - "label": { - "@id": "rdfs:label" - }, - "abstract": { - "@id": "core:abstract" - }, - "combined_text": { - "@id": "core:combined_text" - }, - "full_text": { - "@id": "core:full_text" - }, - "title": { - "@id": "core:title" - }, - "publication": { - "@type": "@id", - "@id": "core:publication" - }, - "triples": { - "@type": "@id", - "@id": "core:triples" - }, - "adverse_effects": { - "@type": "@id" - }, - "mechanism": { - "@type": "@id" - }, - "object": { - "@type": "@id", - "@id": "core:object" - }, - "object_qualifier": { - "@type": "@id", - "@id": "core:object_qualifier" - }, - "predicate": { - "@type": "@id", - "@id": "core:predicate" - }, - "qualifier": { - "@id": "core:qualifier" - }, - "subject": { - "@type": "@id", - "@id": "core:subject" - }, - "subject_qualifier": { - "@type": "@id", - "@id": "core:subject_qualifier" - }, - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } - } -} diff --git a/projects/treatment/jsonld/treatment.jsonld b/projects/treatment/jsonld/treatment.jsonld deleted file mode 100644 index 79f6be1a5..000000000 --- a/projects/treatment/jsonld/treatment.jsonld +++ /dev/null @@ -1,1587 +0,0 @@ -{ - "name": "treatment-template", - "description": "A template for MAXO treatments", - "title": "MAXO treatment Template", - "id": "http://w3id.org/ontogpt/treatment", - "imports": [ - "linkml:types", - "core" - ], - "license": "https://creativecommons.org/publicdomain/zero/1.0/", - "prefixes": [ - { - "prefix_prefix": "linkml", - "prefix_reference": "https://w3id.org/linkml/" - }, - { - "prefix_prefix": "treatment", - "prefix_reference": "http://w3id.org/ontogpt/treatments/" - } - ], - "default_prefix": "treatment", - "default_range": "string", - "types": [ - { - "name": "string", - "definition_uri": "https://w3id.org/linkml/String", - "description": "A character string", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Text" - ], - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "@type": "TypeDefinition" - }, - { - "name": "integer", - "definition_uri": "https://w3id.org/linkml/Integer", - "description": "An integer", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Integer" - ], - "base": "int", - "uri": "http://www.w3.org/2001/XMLSchema#integer", - "@type": "TypeDefinition" - }, - { - "name": "boolean", - "definition_uri": "https://w3id.org/linkml/Boolean", - "description": "A binary (true or false) value", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Boolean" - ], - "base": "Bool", - "uri": "http://www.w3.org/2001/XMLSchema#boolean", - "repr": "bool", - "@type": "TypeDefinition" - }, - { - "name": "float", - "definition_uri": "https://w3id.org/linkml/Float", - "description": "A real number that conforms to the xsd:float specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#float", - "@type": "TypeDefinition" - }, - { - "name": "double", - "definition_uri": "https://w3id.org/linkml/Double", - "description": "A real number that conforms to the xsd:double specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:Float" - ], - "base": "float", - "uri": "http://www.w3.org/2001/XMLSchema#double", - "@type": "TypeDefinition" - }, - { - "name": "decimal", - "definition_uri": "https://w3id.org/linkml/Decimal", - "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "broad_mappings": [ - "schema:Number" - ], - "base": "Decimal", - "uri": "http://www.w3.org/2001/XMLSchema#decimal", - "@type": "TypeDefinition" - }, - { - "name": "time", - "definition_uri": "https://w3id.org/linkml/Time", - "description": "A time object represents a (local) time of day, independent of any particular day", - "notes": [ - "URI is dateTime because OWL reasoners do not work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Time" - ], - "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#time", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date", - "definition_uri": "https://w3id.org/linkml/Date", - "description": "a date (year, month and day) in an idealized calendar", - "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:Date" - ], - "base": "XSDDate", - "uri": "http://www.w3.org/2001/XMLSchema#date", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "datetime", - "definition_uri": "https://w3id.org/linkml/Datetime", - "description": "The combination of a date and time", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "exact_mappings": [ - "schema:DateTime" - ], - "base": "XSDDateTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "date_or_datetime", - "definition_uri": "https://w3id.org/linkml/DateOrDatetime", - "description": "Either a date or a datetime", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "https://w3id.org/linkml/DateOrDatetime", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uriorcurie", - "definition_uri": "https://w3id.org/linkml/Uriorcurie", - "description": "a URI or a CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "URIorCURIE", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "curie", - "definition_uri": "https://w3id.org/linkml/Curie", - "conforms_to": "https://www.w3.org/TR/curie/", - "description": "a compact URI", - "comments": [ - "in RDF serializations this MUST be expanded to a URI", - "in non-RDF serializations MAY be serialized as the compact representation" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "Curie", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "uri", - "definition_uri": "https://w3id.org/linkml/Uri", - "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", - "description": "a complete URI", - "comments": [ - "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "close_mappings": [ - "schema:URL" - ], - "base": "URI", - "uri": "http://www.w3.org/2001/XMLSchema#anyURI", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "ncname", - "definition_uri": "https://w3id.org/linkml/Ncname", - "description": "Prefix part of CURIE", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NCName", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "objectidentifier", - "definition_uri": "https://w3id.org/linkml/Objectidentifier", - "description": "A URI or CURIE that represents an object in the model.", - "comments": [ - "Used for inheritance and type checking" - ], - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "ElementIdentifier", - "uri": "http://www.w3.org/ns/shex#iri", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "nodeidentifier", - "definition_uri": "https://w3id.org/linkml/Nodeidentifier", - "description": "A URI, CURIE or BNODE that represents a node in a model.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "NodeIdentifier", - "uri": "http://www.w3.org/ns/shex#nonLiteral", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpointer", - "definition_uri": "https://w3id.org/linkml/Jsonpointer", - "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", - "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "jsonpath", - "definition_uri": "https://w3id.org/linkml/Jsonpath", - "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", - "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - }, - { - "name": "sparqlpath", - "definition_uri": "https://w3id.org/linkml/Sparqlpath", - "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", - "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", - "from_schema": "https://w3id.org/linkml/types", - "imported_from": "linkml:types", - "base": "str", - "uri": "http://www.w3.org/2001/XMLSchema#string", - "repr": "str", - "@type": "TypeDefinition" - } - ], - "enums": [ - { - "name": "NCITDrugType", - "definition_uri": "http://w3id.org/ontogpt/treatments/NCITDrugType", - "from_schema": "http://w3id.org/ontogpt/treatment", - "reachable_from": { - "source_ontology": "obo:ncit", - "source_nodes": [ - "NCIT:C1908" - ] - } - }, - { - "name": "NCITTreatmentType", - "definition_uri": "http://w3id.org/ontogpt/treatments/NCITTreatmentType", - "from_schema": "http://w3id.org/ontogpt/treatment", - "reachable_from": { - "source_ontology": "obo:ncit", - "source_nodes": [ - "NCIT:C25218" - ] - } - }, - { - "name": "NCITTActivityType", - "definition_uri": "http://w3id.org/ontogpt/treatments/NCITTActivityType", - "from_schema": "http://w3id.org/ontogpt/treatment", - "reachable_from": { - "source_ontology": "obo:ncit", - "source_nodes": [ - "NCIT:C43431" - ] - } - }, - { - "name": "MAXOActionType", - "definition_uri": "http://w3id.org/ontogpt/treatments/MAXOActionType", - "from_schema": "http://w3id.org/ontogpt/treatment", - "reachable_from": { - "source_ontology": "obo:maxo", - "source_nodes": [ - "MAXO:0000001" - ] - } - }, - { - "name": "MESHTherapeuticType", - "definition_uri": "http://w3id.org/ontogpt/treatments/MESHTherapeuticType", - "from_schema": "http://w3id.org/ontogpt/treatment", - "reachable_from": { - "source_ontology": "obo:mesh", - "source_nodes": [ - "MESH:D013812" - ] - } - }, - { - "name": "CHEBIDrugType", - "definition_uri": "http://w3id.org/ontogpt/treatments/CHEBIDrugType", - "from_schema": "http://w3id.org/ontogpt/treatment", - "reachable_from": { - "source_ontology": "obo:chebi", - "source_nodes": [ - "CHEBI:23888" - ], - "relationship_types": [ - "rdfs:subClassOf", - "RO:0000087" - ] - } - }, - { - "name": "NullDataOptions", - "definition_uri": "http://w3id.org/ontogpt/core/NullDataOptions", - "from_schema": "http://w3id.org/ontogpt/core", - "permissible_values": [ - { - "text": "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "meaning": "NCIT:C149701" - }, - { - "text": "NOT_APPLICABLE", - "meaning": "NCIT:C18902", - "aliases": [ - "not applicable", - "N/A" - ] - }, - { - "text": "NOT_MENTIONED" - } - ] - } - ], - "slots": [ - { - "name": "diseaseTreatmentSummary__disease", - "description": "the name of the disease that is treated.", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/disease", - "alias": "disease", - "owner": "DiseaseTreatmentSummary", - "domain_of": [ - "DiseaseTreatmentSummary" - ], - "range": "Disease", - "@type": "SlotDefinition" - }, - { - "name": "diseaseTreatmentSummary__drugs", - "description": "semicolon-separated list of named small molecule drugs", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/drugs", - "multivalued": true, - "alias": "drugs", - "owner": "DiseaseTreatmentSummary", - "domain_of": [ - "DiseaseTreatmentSummary" - ], - "range": "Drug", - "@type": "SlotDefinition" - }, - { - "name": "diseaseTreatmentSummary__treatments", - "annotations": [ - { - "tag": "prompt.examples", - "value": "Imatinib, exercise, surgery", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of therapies and treatments are indicated for treating the disease.", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/treatments", - "multivalued": true, - "alias": "treatments", - "owner": "DiseaseTreatmentSummary", - "domain_of": [ - "DiseaseTreatmentSummary" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "diseaseTreatmentSummary__contraindications", - "annotations": [ - { - "tag": "prompt.examples", - "value": "Beta-blockers, exercise, surgery", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/contraindications", - "multivalued": true, - "alias": "contraindications", - "owner": "DiseaseTreatmentSummary", - "domain_of": [ - "DiseaseTreatmentSummary" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "diseaseTreatmentSummary__treatment_mechanisms", - "annotations": [ - { - "tag": "prompt.separator", - "value": "*", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of treatment to asterisk-separated mechanism associations", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/treatment_mechanisms", - "multivalued": true, - "alias": "treatment_mechanisms", - "owner": "DiseaseTreatmentSummary", - "domain_of": [ - "DiseaseTreatmentSummary" - ], - "range": "TreatmentMechanism", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "diseaseTreatmentSummary__treatment_efficacies", - "annotations": [ - { - "tag": "prompt.separator", - "value": "*", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/treatment_efficacies", - "multivalued": true, - "alias": "treatment_efficacies", - "owner": "DiseaseTreatmentSummary", - "domain_of": [ - "DiseaseTreatmentSummary" - ], - "range": "TreatmentEfficacy", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "diseaseTreatmentSummary__treatment_adverse_effects", - "annotations": [ - { - "tag": "prompt.separator", - "value": "*", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/treatment_adverse_effects", - "multivalued": true, - "alias": "treatment_adverse_effects", - "owner": "DiseaseTreatmentSummary", - "domain_of": [ - "DiseaseTreatmentSummary" - ], - "range": "TreatmentAdverseEffect", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "treatmentMechanism__treatment", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/treatment", - "alias": "treatment", - "owner": "TreatmentMechanism", - "domain_of": [ - "TreatmentMechanism" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "treatmentMechanism__mechanism", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/mechanism", - "alias": "mechanism", - "owner": "TreatmentMechanism", - "domain_of": [ - "TreatmentMechanism" - ], - "range": "Mechanism", - "@type": "SlotDefinition" - }, - { - "name": "treatmentAdverseEffect__treatment", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/treatment", - "alias": "treatment", - "owner": "TreatmentAdverseEffect", - "domain_of": [ - "TreatmentAdverseEffect" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "treatmentAdverseEffect__adverse_effects", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/adverse_effects", - "multivalued": true, - "alias": "adverse_effects", - "owner": "TreatmentAdverseEffect", - "domain_of": [ - "TreatmentAdverseEffect" - ], - "range": "AdverseEffect", - "@type": "SlotDefinition" - }, - { - "name": "treatmentEfficacy__treatment", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/treatment", - "alias": "treatment", - "owner": "TreatmentEfficacy", - "domain_of": [ - "TreatmentEfficacy" - ], - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "treatmentEfficacy__efficacy", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slot_uri": "http://w3id.org/ontogpt/treatments/efficacy", - "alias": "efficacy", - "owner": "TreatmentEfficacy", - "domain_of": [ - "TreatmentEfficacy" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_id", - "alias": "input_id", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_title", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_title", - "alias": "input_title", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__input_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/input_text", - "alias": "input_text", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__raw_completion_output", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/raw_completion_output", - "alias": "raw_completion_output", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__prompt", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/prompt", - "alias": "prompt", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__extracted_object", - "description": "The complex objects extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/extracted_object", - "alias": "extracted_object", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "extractionResult__named_entities", - "description": "Named entities extracted from the text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/named_entities", - "multivalued": true, - "alias": "named_entities", - "owner": "ExtractionResult", - "domain_of": [ - "ExtractionResult" - ], - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "identifier": true, - "alias": "id", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "required": true, - "@type": "SlotDefinition" - }, - { - "name": "namedEntity__label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "from_schema": "http://w3id.org/ontogpt/core", - "aliases": [ - "name" - ], - "mappings": [ - "http://example.org/UNKNOWN/rdfs/label" - ], - "slot_uri": "http://example.org/UNKNOWN/rdfs/label", - "alias": "label", - "owner": "NamedEntity", - "domain_of": [ - "NamedEntity" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject", - "alias": "subject", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__predicate", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/predicate", - "alias": "predicate", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "triple__object", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object", - "alias": "object", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/qualifier", - "alias": "qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "triple__subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_qualifier", - "alias": "subject_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "triple__object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_qualifier", - "alias": "object_qualifier", - "owner": "Triple", - "domain_of": [ - "Triple" - ], - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/publication", - "alias": "publication", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "textWithTriples__triples", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/triples", - "multivalued": true, - "alias": "triples", - "owner": "TextWithTriples", - "domain_of": [ - "TextWithTriples" - ], - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - }, - { - "name": "publication__id", - "description": "The publication identifier", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/id", - "alias": "id", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__title", - "description": "The title of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/title", - "alias": "title", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__abstract", - "description": "The abstract of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/abstract", - "alias": "abstract", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__combined_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/combined_text", - "alias": "combined_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "publication__full_text", - "description": "The full text of the publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/full_text", - "alias": "full_text", - "owner": "Publication", - "domain_of": [ - "Publication" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__subject_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/subject_text", - "alias": "subject_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_id", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_id", - "alias": "object_id", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "annotatorResult__object_text", - "from_schema": "http://w3id.org/ontogpt/core", - "slot_uri": "http://w3id.org/ontogpt/core/object_text", - "alias": "object_text", - "owner": "AnnotatorResult", - "domain_of": [ - "AnnotatorResult" - ], - "range": "string", - "@type": "SlotDefinition" - } - ], - "classes": [ - { - "name": "DiseaseTreatmentSummary", - "definition_uri": "http://w3id.org/ontogpt/treatments/DiseaseTreatmentSummary", - "from_schema": "http://w3id.org/ontogpt/treatment", - "slots": [ - "diseaseTreatmentSummary__disease", - "diseaseTreatmentSummary__drugs", - "diseaseTreatmentSummary__treatments", - "diseaseTreatmentSummary__contraindications", - "diseaseTreatmentSummary__treatment_mechanisms", - "diseaseTreatmentSummary__treatment_efficacies", - "diseaseTreatmentSummary__treatment_adverse_effects" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "disease", - "description": "the name of the disease that is treated.", - "range": "Disease", - "@type": "SlotDefinition" - }, - { - "name": "drugs", - "description": "semicolon-separated list of named small molecule drugs", - "multivalued": true, - "range": "Drug", - "@type": "SlotDefinition" - }, - { - "name": "treatments", - "annotations": [ - { - "tag": "prompt.examples", - "value": "Imatinib, exercise, surgery", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of therapies and treatments are indicated for treating the disease.", - "multivalued": true, - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "contraindications", - "annotations": [ - { - "tag": "prompt.examples", - "value": "Beta-blockers, exercise, surgery", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.", - "multivalued": true, - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "treatment_mechanisms", - "annotations": [ - { - "tag": "prompt.separator", - "value": "*", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of treatment to asterisk-separated mechanism associations", - "multivalued": true, - "range": "TreatmentMechanism", - "@type": "SlotDefinition" - }, - { - "name": "treatment_efficacies", - "annotations": [ - { - "tag": "prompt.separator", - "value": "*", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective", - "multivalued": true, - "range": "TreatmentEfficacy", - "@type": "SlotDefinition" - }, - { - "name": "treatment_adverse_effects", - "annotations": [ - { - "tag": "prompt.separator", - "value": "*", - "@type": "Annotation" - } - ], - "description": "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea", - "multivalued": true, - "range": "TreatmentAdverseEffect", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/treatments/DiseaseTreatmentSummary", - "tree_root": true, - "@type": "ClassDefinition" - }, - { - "name": "Gene", - "id_prefixes": [ - "HGNC" - ], - "definition_uri": "http://w3id.org/ontogpt/treatments/Gene", - "annotations": [ - { - "tag": "annotators", - "value": "gilda:, obo:sql:hgnc, bioportal:hgnc-nr", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/treatments/Gene", - "@type": "ClassDefinition" - }, - { - "name": "Symptom", - "id_prefixes": [ - "HP" - ], - "definition_uri": "http://w3id.org/ontogpt/treatments/Symptom", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:hp", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/treatments/Symptom", - "@type": "ClassDefinition" - }, - { - "name": "Disease", - "definition_uri": "http://w3id.org/ontogpt/treatments/Disease", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:mondo", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/treatments/Disease", - "@type": "ClassDefinition" - }, - { - "name": "AdverseEffect", - "definition_uri": "http://w3id.org/ontogpt/treatments/AdverseEffect", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:hp, sqlite:obo:ncit", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/treatments/AdverseEffect", - "@type": "ClassDefinition" - }, - { - "name": "Treatment", - "definition_uri": "http://w3id.org/ontogpt/treatments/Treatment", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "NamedEntity", - "values_from": [ - "NCITDrugType", - "NCITTreatmentType", - "NCITActivityType", - "MAXOTreatmentType", - "MESHTherapeuticType", - "CHEBIDrugType" - ], - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/treatments/Treatment", - "@type": "ClassDefinition" - }, - { - "name": "Mechanism", - "definition_uri": "http://w3id.org/ontogpt/treatments/Mechanism", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/treatments/Mechanism", - "@type": "ClassDefinition" - }, - { - "name": "Drug", - "definition_uri": "http://w3id.org/ontogpt/treatments/Drug", - "annotations": [ - { - "tag": "annotators", - "value": "sqlite:obo:chebi, sqlite:obo:drugbank", - "@type": "Annotation" - } - ], - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/treatments/Drug", - "@type": "ClassDefinition" - }, - { - "name": "TreatmentMechanism", - "definition_uri": "http://w3id.org/ontogpt/treatments/TreatmentMechanism", - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "CompoundExpression", - "slots": [ - "treatmentMechanism__treatment", - "treatmentMechanism__mechanism" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "treatment", - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "mechanism", - "range": "Mechanism", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/treatments/TreatmentMechanism", - "@type": "ClassDefinition" - }, - { - "name": "TreatmentAdverseEffect", - "definition_uri": "http://w3id.org/ontogpt/treatments/TreatmentAdverseEffect", - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "CompoundExpression", - "slots": [ - "treatmentAdverseEffect__treatment", - "treatmentAdverseEffect__adverse_effects" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "treatment", - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "adverse_effects", - "multivalued": true, - "range": "AdverseEffect", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/treatments/TreatmentAdverseEffect", - "@type": "ClassDefinition" - }, - { - "name": "TreatmentEfficacy", - "definition_uri": "http://w3id.org/ontogpt/treatments/TreatmentEfficacy", - "from_schema": "http://w3id.org/ontogpt/treatment", - "is_a": "CompoundExpression", - "slots": [ - "treatmentEfficacy__treatment", - "treatmentEfficacy__efficacy" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "treatment", - "range": "Treatment", - "@type": "SlotDefinition" - }, - { - "name": "efficacy", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/treatments/TreatmentEfficacy", - "@type": "ClassDefinition" - }, - { - "name": "Any", - "definition_uri": "http://w3id.org/ontogpt/core/Any", - "from_schema": "http://w3id.org/ontogpt/core", - "mappings": [ - "linkml:Any" - ], - "slot_usage": {}, - "class_uri": "https://w3id.org/linkml/Any", - "@type": "ClassDefinition" - }, - { - "name": "ExtractionResult", - "definition_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "description": "A result of extracting knowledge on text", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "extractionResult__input_id", - "extractionResult__input_title", - "extractionResult__input_text", - "extractionResult__raw_completion_output", - "extractionResult__prompt", - "extractionResult__extracted_object", - "extractionResult__named_entities" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "input_id", - "@type": "SlotDefinition" - }, - { - "name": "input_title", - "@type": "SlotDefinition" - }, - { - "name": "input_text", - "@type": "SlotDefinition" - }, - { - "name": "raw_completion_output", - "@type": "SlotDefinition" - }, - { - "name": "prompt", - "@type": "SlotDefinition" - }, - { - "name": "extracted_object", - "description": "The complex objects extracted from the text", - "range": "Any", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "named_entities", - "description": "Named entities extracted from the text", - "multivalued": true, - "range": "Any", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/ExtractionResult", - "@type": "ClassDefinition" - }, - { - "name": "NamedEntity", - "definition_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "description": "A unique identifier for the named entity", - "comments": [ - "this is populated during the grounding and normalization step" - ], - "identifier": true, - "@type": "SlotDefinition" - }, - { - "name": "label", - "annotations": [ - { - "tag": "owl", - "value": "AnnotationProperty, AnnotationAssertion", - "@type": "Annotation" - } - ], - "description": "The label (name) of the named thing", - "aliases": [ - "name" - ], - "slot_uri": "rdfs:label", - "range": "string", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/NamedEntity", - "@type": "ClassDefinition" - }, - { - "name": "CompoundExpression", - "definition_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "from_schema": "http://w3id.org/ontogpt/core", - "abstract": true, - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/CompoundExpression", - "@type": "ClassDefinition" - }, - { - "name": "Triple", - "definition_uri": "http://w3id.org/ontogpt/core/Triple", - "description": "Abstract parent for Relation Extraction tasks", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "CompoundExpression", - "abstract": true, - "slots": [ - "triple__subject", - "triple__predicate", - "triple__object", - "triple__qualifier", - "triple__subject_qualifier", - "triple__object_qualifier" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "predicate", - "range": "RelationshipType", - "@type": "SlotDefinition" - }, - { - "name": "object", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "qualifier", - "description": "A qualifier for the statements, e.g. \"NOT\" for negation", - "range": "string", - "@type": "SlotDefinition" - }, - { - "name": "subject_qualifier", - "description": "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - }, - { - "name": "object_qualifier", - "description": "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"", - "range": "NamedEntity", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Triple", - "@type": "ClassDefinition" - }, - { - "name": "TextWithTriples", - "definition_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "textWithTriples__publication", - "textWithTriples__triples" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "publication", - "annotations": [ - { - "tag": "prompt.skip", - "value": "true", - "@type": "Annotation" - } - ], - "range": "Publication", - "inlined": true, - "@type": "SlotDefinition" - }, - { - "name": "triples", - "multivalued": true, - "range": "Triple", - "inlined": true, - "inlined_as_list": true, - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/TextWithTriples", - "@type": "ClassDefinition" - }, - { - "name": "RelationshipType", - "id_prefixes": [ - "RO", - "biolink" - ], - "definition_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "from_schema": "http://w3id.org/ontogpt/core", - "is_a": "NamedEntity", - "slots": [ - "namedEntity__id", - "namedEntity__label" - ], - "slot_usage": {}, - "class_uri": "http://w3id.org/ontogpt/core/RelationshipType", - "@type": "ClassDefinition" - }, - { - "name": "Publication", - "definition_uri": "http://w3id.org/ontogpt/core/Publication", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "publication__id", - "publication__title", - "publication__abstract", - "publication__combined_text", - "publication__full_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "id", - "description": "The publication identifier", - "@type": "SlotDefinition" - }, - { - "name": "title", - "description": "The title of the publication", - "@type": "SlotDefinition" - }, - { - "name": "abstract", - "description": "The abstract of the publication", - "@type": "SlotDefinition" - }, - { - "name": "combined_text", - "@type": "SlotDefinition" - }, - { - "name": "full_text", - "description": "The full text of the publication", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/Publication", - "@type": "ClassDefinition" - }, - { - "name": "AnnotatorResult", - "definition_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "from_schema": "http://w3id.org/ontogpt/core", - "slots": [ - "annotatorResult__subject_text", - "annotatorResult__object_id", - "annotatorResult__object_text" - ], - "slot_usage": {}, - "attributes": [ - { - "name": "subject_text", - "@type": "SlotDefinition" - }, - { - "name": "object_id", - "@type": "SlotDefinition" - }, - { - "name": "object_text", - "@type": "SlotDefinition" - } - ], - "class_uri": "http://w3id.org/ontogpt/core/AnnotatorResult", - "@type": "ClassDefinition" - } - ], - "metamodel_version": "1.7.0", - "source_file": "treatment.yaml", - "source_file_date": "2023-06-17T15:11:19", - "source_file_size": 4485, - "generation_date": "2023-08-07T10:56:36", - "keywords": [ - "treatments", - "drugs", - "therapies" - ], - "@type": "SchemaDefinition", - "@context": [ - "projects/treatment/jsonld/treatment.context.jsonld", - "https://w3id.org/linkml/types.context.jsonld", - "core.context.jsonld", - { - "@base": "http://w3id.org/ontogpt/treatments/" - } - ] -} diff --git a/projects/treatment/jsonschema/treatment.schema.json b/projects/treatment/jsonschema/treatment.schema.json deleted file mode 100644 index d63296511..000000000 --- a/projects/treatment/jsonschema/treatment.schema.json +++ /dev/null @@ -1,457 +0,0 @@ -{ - "$defs": { - "AdverseEffect": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "AdverseEffect", - "type": "object" - }, - "AnnotatorResult": { - "additionalProperties": false, - "description": "", - "properties": { - "object_id": { - "type": "string" - }, - "object_text": { - "type": "string" - }, - "subject_text": { - "type": "string" - } - }, - "title": "AnnotatorResult", - "type": "object" - }, - "Any": { - "additionalProperties": true, - "description": "", - "title": "Any", - "type": "object" - }, - "CHEBIDrugType": { - "description": "", - "enum": [], - "title": "CHEBIDrugType", - "type": "string" - }, - "Disease": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Disease", - "type": "object" - }, - "DiseaseTreatmentSummary": { - "additionalProperties": false, - "description": "", - "properties": { - "contraindications": { - "description": "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.", - "items": { - "type": "string" - }, - "type": "array" - }, - "disease": { - "description": "the name of the disease that is treated.", - "type": "string" - }, - "drugs": { - "description": "semicolon-separated list of named small molecule drugs", - "items": { - "type": "string" - }, - "type": "array" - }, - "treatment_adverse_effects": { - "description": "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea", - "items": { - "$ref": "#/$defs/TreatmentAdverseEffect" - }, - "type": "array" - }, - "treatment_efficacies": { - "description": "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective", - "items": { - "$ref": "#/$defs/TreatmentEfficacy" - }, - "type": "array" - }, - "treatment_mechanisms": { - "description": "semicolon-separated list of treatment to asterisk-separated mechanism associations", - "items": { - "$ref": "#/$defs/TreatmentMechanism" - }, - "type": "array" - }, - "treatments": { - "description": "semicolon-separated list of therapies and treatments are indicated for treating the disease.", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "DiseaseTreatmentSummary", - "type": "object" - }, - "Drug": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Drug", - "type": "object" - }, - "ExtractionResult": { - "additionalProperties": false, - "description": "A result of extracting knowledge on text", - "properties": { - "extracted_object": { - "$ref": "#/$defs/Any", - "description": "The complex objects extracted from the text" - }, - "input_id": { - "type": "string" - }, - "input_text": { - "type": "string" - }, - "input_title": { - "type": "string" - }, - "named_entities": { - "description": "Named entities extracted from the text", - "items": { - "$ref": "#/$defs/Any" - }, - "type": "array" - }, - "prompt": { - "type": "string" - }, - "raw_completion_output": { - "type": "string" - } - }, - "title": "ExtractionResult", - "type": "object" - }, - "Gene": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Gene", - "type": "object" - }, - "MAXOActionType": { - "description": "", - "enum": [], - "title": "MAXOActionType", - "type": "string" - }, - "MESHTherapeuticType": { - "description": "", - "enum": [], - "title": "MESHTherapeuticType", - "type": "string" - }, - "Mechanism": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Mechanism", - "type": "object" - }, - "NCITDrugType": { - "description": "", - "enum": [], - "title": "NCITDrugType", - "type": "string" - }, - "NCITTActivityType": { - "description": "", - "enum": [], - "title": "NCITTActivityType", - "type": "string" - }, - "NCITTreatmentType": { - "description": "", - "enum": [], - "title": "NCITTreatmentType", - "type": "string" - }, - "NullDataOptions": { - "description": "", - "enum": [ - "UNSPECIFIED_METHOD_OF_ADMINISTRATION", - "NOT_APPLICABLE", - "NOT_MENTIONED" - ], - "title": "NullDataOptions", - "type": "string" - }, - "Publication": { - "additionalProperties": false, - "description": "", - "properties": { - "abstract": { - "description": "The abstract of the publication", - "type": "string" - }, - "combined_text": { - "type": "string" - }, - "full_text": { - "description": "The full text of the publication", - "type": "string" - }, - "id": { - "description": "The publication identifier", - "type": "string" - }, - "title": { - "description": "The title of the publication", - "type": "string" - } - }, - "title": "Publication", - "type": "object" - }, - "RelationshipType": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "RelationshipType", - "type": "object" - }, - "Symptom": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Symptom", - "type": "object" - }, - "TextWithTriples": { - "additionalProperties": false, - "description": "", - "properties": { - "publication": { - "$ref": "#/$defs/Publication" - }, - "triples": { - "items": { - "$ref": "#/$defs/Triple" - }, - "type": "array" - } - }, - "title": "TextWithTriples", - "type": "object" - }, - "Treatment": { - "additionalProperties": false, - "description": "", - "properties": { - "id": { - "description": "A unique identifier for the named entity", - "type": "string" - }, - "label": { - "description": "The label (name) of the named thing", - "type": "string" - } - }, - "required": [ - "id" - ], - "title": "Treatment", - "type": "object" - }, - "TreatmentAdverseEffect": { - "additionalProperties": false, - "description": "", - "properties": { - "adverse_effects": { - "items": { - "type": "string" - }, - "type": "array" - }, - "treatment": { - "type": "string" - } - }, - "title": "TreatmentAdverseEffect", - "type": "object" - }, - "TreatmentEfficacy": { - "additionalProperties": false, - "description": "", - "properties": { - "efficacy": { - "type": "string" - }, - "treatment": { - "type": "string" - } - }, - "title": "TreatmentEfficacy", - "type": "object" - }, - "TreatmentMechanism": { - "additionalProperties": false, - "description": "", - "properties": { - "mechanism": { - "type": "string" - }, - "treatment": { - "type": "string" - } - }, - "title": "TreatmentMechanism", - "type": "object" - } - }, - "$id": "http://w3id.org/ontogpt/treatment", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": { - "contraindications": { - "description": "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.", - "items": { - "type": "string" - }, - "type": "array" - }, - "disease": { - "description": "the name of the disease that is treated.", - "type": "string" - }, - "drugs": { - "description": "semicolon-separated list of named small molecule drugs", - "items": { - "type": "string" - }, - "type": "array" - }, - "treatment_adverse_effects": { - "description": "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea", - "items": { - "$ref": "#/$defs/TreatmentAdverseEffect" - }, - "type": "array" - }, - "treatment_efficacies": { - "description": "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective", - "items": { - "$ref": "#/$defs/TreatmentEfficacy" - }, - "type": "array" - }, - "treatment_mechanisms": { - "description": "semicolon-separated list of treatment to asterisk-separated mechanism associations", - "items": { - "$ref": "#/$defs/TreatmentMechanism" - }, - "type": "array" - }, - "treatments": { - "description": "semicolon-separated list of therapies and treatments are indicated for treating the disease.", - "items": { - "type": "string" - }, - "type": "array" - } - }, - "title": "treatment-template", - "type": "object", - "version": null -} \ No newline at end of file diff --git a/projects/treatment/owl/treatment.owl.ttl b/projects/treatment/owl/treatment.owl.ttl deleted file mode 100644 index 3ed1f1492..000000000 --- a/projects/treatment/owl/treatment.owl.ttl +++ /dev/null @@ -1,576 +0,0 @@ -@prefix IAO: <http://purl.obolibrary.org/obo/IAO_> . -@prefix linkml: <https://w3id.org/linkml/> . -@prefix owl: <http://www.w3.org/2002/07/owl#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix skos: <http://www.w3.org/2004/02/skos/core#> . -@prefix treatment: <http://w3id.org/ontogpt/treatments/> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/treatment> a owl:Ontology ; - rdfs:label "treatment-template" ; - IAO:0000700 <http://w3id.org/ontogpt/core/AnnotatorResult>, - <http://w3id.org/ontogpt/core/Any>, - <http://w3id.org/ontogpt/core/CompoundExpression>, - <http://w3id.org/ontogpt/core/ExtractionResult>, - <http://w3id.org/ontogpt/core/NamedEntity>, - <http://w3id.org/ontogpt/core/Publication>, - <http://w3id.org/ontogpt/core/TextWithTriples>, - treatment:DiseaseTreatmentSummary ; - linkml:classes "{'DiseaseTreatmentSummary': ClassDefinition(name='DiseaseTreatmentSummary', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/DiseaseTreatmentSummary', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['diseaseTreatmentSummary__disease', 'diseaseTreatmentSummary__drugs', 'diseaseTreatmentSummary__treatments', 'diseaseTreatmentSummary__contraindications', 'diseaseTreatmentSummary__treatment_mechanisms', 'diseaseTreatmentSummary__treatment_efficacies', 'diseaseTreatmentSummary__treatment_adverse_effects'], slot_usage={}, attributes={'disease': SlotDefinition(name='disease', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the disease that is treated.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'drugs': SlotDefinition(name='drugs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of named small molecule drugs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Drug', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatments': SlotDefinition(name='treatments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.examples': Annotation(tag='prompt.examples', value='Imatinib, exercise, surgery', extensions={}, annotations={})}, description='semicolon-separated list of therapies and treatments are indicated for treating the disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'contraindications': SlotDefinition(name='contraindications', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.examples': Annotation(tag='prompt.examples', value='Beta-blockers, exercise, surgery', extensions={}, annotations={})}, description='semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_mechanisms': SlotDefinition(name='treatment_mechanisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to asterisk-separated mechanism associations', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentMechanism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_efficacies': SlotDefinition(name='treatment_efficacies', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentEfficacy', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_adverse_effects': SlotDefinition(name='treatment_adverse_effects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentAdverseEffect', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='treatment:DiseaseTreatmentSummary', subclass_of=None, union_of=[], defining_slots=[], tree_root=True, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Gene': ClassDefinition(name='Gene', id_prefixes=['HGNC'], definition_uri='http://w3id.org/ontogpt/treatments/Gene', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='gilda:, obo:sql:hgnc, bioportal:hgnc-nr', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='treatment:Gene', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Symptom': ClassDefinition(name='Symptom', id_prefixes=['HP'], definition_uri='http://w3id.org/ontogpt/treatments/Symptom', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hp', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='treatment:Symptom', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Disease': ClassDefinition(name='Disease', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/Disease', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:mondo', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='treatment:Disease', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AdverseEffect': ClassDefinition(name='AdverseEffect', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/AdverseEffect', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:hp, sqlite:obo:ncit', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='treatment:AdverseEffect', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Treatment': ClassDefinition(name='Treatment', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/Treatment', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=['NCITDrugType', 'NCITTreatmentType', 'NCITActivityType', 'MAXOTreatmentType', 'MESHTherapeuticType', 'CHEBIDrugType'], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='treatment:Treatment', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Mechanism': ClassDefinition(name='Mechanism', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/Mechanism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='treatment:Mechanism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Drug': ClassDefinition(name='Drug', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/Drug', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'annotators': Annotation(tag='annotators', value='sqlite:obo:chebi, sqlite:obo:drugbank', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='treatment:Drug', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TreatmentMechanism': ClassDefinition(name='TreatmentMechanism', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/TreatmentMechanism', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['treatmentMechanism__treatment', 'treatmentMechanism__mechanism'], slot_usage={}, attributes={'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'mechanism': SlotDefinition(name='mechanism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Mechanism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='treatment:TreatmentMechanism', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TreatmentAdverseEffect': ClassDefinition(name='TreatmentAdverseEffect', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/TreatmentAdverseEffect', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['treatmentAdverseEffect__treatment', 'treatmentAdverseEffect__adverse_effects'], slot_usage={}, attributes={'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'adverse_effects': SlotDefinition(name='adverse_effects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='AdverseEffect', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='treatment:TreatmentAdverseEffect', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TreatmentEfficacy': ClassDefinition(name='TreatmentEfficacy', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/TreatmentEfficacy', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['treatmentEfficacy__treatment', 'treatmentEfficacy__efficacy'], slot_usage={}, attributes={'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'efficacy': SlotDefinition(name='efficacy', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='treatment:TreatmentEfficacy', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Any': ClassDefinition(name='Any', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Any', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['linkml:Any'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='linkml:Any', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'ExtractionResult': ClassDefinition(name='ExtractionResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/ExtractionResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A result of extracting knowledge on text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['extractionResult__input_id', 'extractionResult__input_title', 'extractionResult__input_text', 'extractionResult__raw_completion_output', 'extractionResult__prompt', 'extractionResult__extracted_object', 'extractionResult__named_entities'], slot_usage={}, attributes={'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:ExtractionResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'NamedEntity': ClassDefinition(name='NamedEntity', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NamedEntity', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:NamedEntity', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'CompoundExpression': ClassDefinition(name='CompoundExpression', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/CompoundExpression', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=[], slot_usage={}, attributes={}, class_uri='core:CompoundExpression', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Triple': ClassDefinition(name='Triple', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Triple', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Abstract parent for Relation Extraction tasks', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='CompoundExpression', abstract=True, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['triple__subject', 'triple__predicate', 'triple__object', 'triple__qualifier', 'triple__subject_qualifier', 'triple__object_qualifier'], slot_usage={}, attributes={'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Triple', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'TextWithTriples': ClassDefinition(name='TextWithTriples', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/TextWithTriples', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['textWithTriples__publication', 'textWithTriples__triples'], slot_usage={}, attributes={'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:TextWithTriples', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'RelationshipType': ClassDefinition(name='RelationshipType', id_prefixes=['RO', 'biolink'], definition_uri='http://w3id.org/ontogpt/core/RelationshipType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a='NamedEntity', abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['namedEntity__id', 'namedEntity__label'], slot_usage={}, attributes={}, class_uri='core:RelationshipType', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'Publication': ClassDefinition(name='Publication', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/Publication', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['publication__id', 'publication__title', 'publication__abstract', 'publication__combined_text', 'publication__full_text'], slot_usage={}, attributes={'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:Publication', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'AnnotatorResult': ClassDefinition(name='AnnotatorResult', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/AnnotatorResult', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['annotatorResult__subject_text', 'annotatorResult__object_id', 'annotatorResult__object_text'], slot_usage={}, attributes={'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, class_uri='core:AnnotatorResult', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; - linkml:enums "{'NCITDrugType': EnumDefinition(name='NCITDrugType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/NCITDrugType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:ncit', source_nodes=['NCIT:C1908'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NCITTreatmentType': EnumDefinition(name='NCITTreatmentType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/NCITTreatmentType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:ncit', source_nodes=['NCIT:C25218'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NCITTActivityType': EnumDefinition(name='NCITTActivityType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/NCITTActivityType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:ncit', source_nodes=['NCIT:C43431'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'MAXOActionType': EnumDefinition(name='MAXOActionType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/MAXOActionType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:maxo', source_nodes=['MAXO:0000001'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'MESHTherapeuticType': EnumDefinition(name='MESHTherapeuticType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/MESHTherapeuticType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:mesh', source_nodes=['MESH:D013812'], relationship_types=[], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'CHEBIDrugType': EnumDefinition(name='CHEBIDrugType', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/treatments/CHEBIDrugType', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/treatment', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={}, include=[], minus=[], inherits=[], reachable_from=ReachabilityQuery(source_ontology='obo:chebi', source_nodes=['CHEBI:23888'], relationship_types=['rdfs:subClassOf', 'RO:0000087'], is_direct=None, include_self=None, traverse_up=None), matches=None, concepts=[]), 'NullDataOptions': EnumDefinition(name='NullDataOptions', id_prefixes=[], definition_uri='http://w3id.org/ontogpt/core/NullDataOptions', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='http://w3id.org/ontogpt/core', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'UNSPECIFIED_METHOD_OF_ADMINISTRATION': PermissibleValue(text='UNSPECIFIED_METHOD_OF_ADMINISTRATION', description=None, meaning='NCIT:C149701', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_APPLICABLE': PermissibleValue(text='NOT_APPLICABLE', description=None, meaning='NCIT:C18902', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['not applicable', 'N/A'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'NOT_MENTIONED': PermissibleValue(text='NOT_MENTIONED', description=None, meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; - linkml:id "http://w3id.org/ontogpt/treatment" ; - linkml:imports "core", - "linkml:types" ; - linkml:types "{'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -treatment:CHEBIDrugType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "CHEBIDrugType" ; - owl:unionOf [ rdf:rest () ] . - -treatment:Gene a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Gene" ; - treatment:annotators "gilda:, obo:sql:hgnc, bioportal:hgnc-nr" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -treatment:MAXOActionType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "MAXOActionType" ; - owl:unionOf [ rdf:rest () ] . - -treatment:MESHTherapeuticType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "MESHTherapeuticType" ; - owl:unionOf [ rdf:rest () ] . - -treatment:NCITDrugType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NCITDrugType" ; - owl:unionOf [ rdf:rest () ] . - -treatment:NCITTActivityType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NCITTActivityType" ; - owl:unionOf [ rdf:rest () ] . - -treatment:NCITTreatmentType a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NCITTreatmentType" ; - owl:unionOf [ rdf:rest () ] . - -treatment:Symptom a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Symptom" ; - treatment:annotators "sqlite:obo:hp" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" . - -linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" ; - linkml:attributes "{}" ; - linkml:is_a "element" ; - linkml:mixins "type_expression" . - -linkml:topValue a owl:DatatypeProperty ; - rdfs:label "value" . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AnnotatorResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/object_id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_text> ] ; - linkml:attributes "{'subject_text': SlotDefinition(name='subject_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_id': SlotDefinition(name='object_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_text': SlotDefinition(name='object_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/ExtractionResult> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "ExtractionResult" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/prompt> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_text> ], - [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/named_entities> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Any> ; - owl:onProperty <http://w3id.org/ontogpt/core/extracted_object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/input_id> ] ; - skos:definition "A result of extracting knowledge on text" ; - linkml:attributes "{'input_id': SlotDefinition(name='input_id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_title': SlotDefinition(name='input_title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'input_text': SlotDefinition(name='input_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'raw_completion_output': SlotDefinition(name='raw_completion_output', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'prompt': SlotDefinition(name='prompt', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'extracted_object': SlotDefinition(name='extracted_object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The complex objects extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'named_entities': SlotDefinition(name='named_entities', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Named entities extracted from the text', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Any', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/TextWithTriples> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TextWithTriples" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom <http://w3id.org/ontogpt/core/Triple> ; - owl:onProperty <http://w3id.org/ontogpt/core/triples> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/Publication> ; - owl:onProperty <http://w3id.org/ontogpt/core/publication> ] ; - linkml:attributes "{'publication': SlotDefinition(name='publication', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Publication', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'triples': SlotDefinition(name='triples', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Triple', range_expression=None, enum_range=None, required=None, recommended=None, inlined=True, inlined_as_list=True, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -<http://w3id.org/ontogpt/core/abstract> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "abstract" ; - rdfs:range linkml:String ; - skos:definition "The abstract of the publication" . - -<http://w3id.org/ontogpt/core/combined_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "combined_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/extracted_object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "extracted_object" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "The complex objects extracted from the text" . - -<http://w3id.org/ontogpt/core/full_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "full_text" ; - rdfs:range linkml:String ; - skos:definition "The full text of the publication" . - -<http://w3id.org/ontogpt/core/input_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/input_title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "input_title" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/named_entities> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "named_entities" ; - rdfs:range <http://w3id.org/ontogpt/core/Any> ; - skos:definition "Named entities extracted from the text" . - -<http://w3id.org/ontogpt/core/object> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/object_id> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_id" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/object_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" . - -<http://w3id.org/ontogpt/core/object_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "object_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/predicate> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "predicate" ; - rdfs:range <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/prompt> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "prompt" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/publication> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "publication" ; - treatment:prompt.skip "true" ; - rdfs:range <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "qualifier" ; - rdfs:range linkml:String ; - skos:definition "A qualifier for the statements, e.g. \"NOT\" for negation" . - -<http://w3id.org/ontogpt/core/raw_completion_output> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "raw_completion_output" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/subject> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> . - -<http://w3id.org/ontogpt/core/subject_qualifier> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_qualifier" ; - rdfs:range <http://w3id.org/ontogpt/core/NamedEntity> ; - skos:definition "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" . - -<http://w3id.org/ontogpt/core/subject_text> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "subject_text" ; - rdfs:range linkml:String . - -<http://w3id.org/ontogpt/core/title> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "title" ; - rdfs:range linkml:String ; - skos:definition "The title of the publication" . - -<http://w3id.org/ontogpt/core/triples> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "triples" ; - rdfs:range <http://w3id.org/ontogpt/core/Triple> . - -treatment:DiseaseTreatmentSummary a owl:Class, - linkml:ClassDefinition ; - rdfs:label "DiseaseTreatmentSummary" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom treatment:TreatmentMechanism ; - owl:onProperty treatment:treatment_mechanisms ], - [ a owl:Restriction ; - owl:allValuesFrom treatment:TreatmentAdverseEffect ; - owl:onProperty treatment:treatment_adverse_effects ], - [ a owl:Restriction ; - owl:allValuesFrom treatment:TreatmentEfficacy ; - owl:onProperty treatment:treatment_efficacies ], - [ a owl:Restriction ; - owl:allValuesFrom treatment:Drug ; - owl:onProperty treatment:drugs ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass treatment:Disease ; - owl:onProperty treatment:disease ], - [ a owl:Restriction ; - owl:allValuesFrom treatment:Treatment ; - owl:onProperty treatment:treatments ], - [ a owl:Restriction ; - owl:allValuesFrom treatment:Treatment ; - owl:onProperty treatment:contraindications ] ; - linkml:attributes "{'disease': SlotDefinition(name='disease', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='the name of the disease that is treated.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Disease', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'drugs': SlotDefinition(name='drugs', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='semicolon-separated list of named small molecule drugs', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Drug', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatments': SlotDefinition(name='treatments', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.examples': Annotation(tag='prompt.examples', value='Imatinib, exercise, surgery', extensions={}, annotations={})}, description='semicolon-separated list of therapies and treatments are indicated for treating the disease.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'contraindications': SlotDefinition(name='contraindications', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.examples': Annotation(tag='prompt.examples', value='Beta-blockers, exercise, surgery', extensions={}, annotations={})}, description='semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_mechanisms': SlotDefinition(name='treatment_mechanisms', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to asterisk-separated mechanism associations', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentMechanism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_efficacies': SlotDefinition(name='treatment_efficacies', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentEfficacy', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'treatment_adverse_effects': SlotDefinition(name='treatment_adverse_effects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.separator': Annotation(tag='prompt.separator', value='*', extensions={}, annotations={})}, description='semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='TreatmentAdverseEffect', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -treatment:adverse_effects a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "adverse_effects" ; - rdfs:range treatment:AdverseEffect . - -treatment:contraindications a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "contraindications" ; - treatment:prompt.examples "Beta-blockers, exercise, surgery" ; - rdfs:range treatment:Treatment ; - skos:definition "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects." . - -treatment:disease a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "disease" ; - rdfs:range treatment:Disease ; - skos:definition "the name of the disease that is treated." . - -treatment:drugs a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "drugs" ; - rdfs:range treatment:Drug ; - skos:definition "semicolon-separated list of named small molecule drugs" . - -treatment:efficacy a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "efficacy" ; - rdfs:range linkml:String . - -treatment:mechanism a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "mechanism" ; - rdfs:range treatment:Mechanism . - -treatment:treatment_adverse_effects a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatment_adverse_effects" ; - treatment:prompt.separator "*" ; - rdfs:range treatment:TreatmentAdverseEffect ; - skos:definition "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea" . - -treatment:treatment_efficacies a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatment_efficacies" ; - treatment:prompt.separator "*" ; - rdfs:range treatment:TreatmentEfficacy ; - skos:definition "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective" . - -treatment:treatment_mechanisms a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatment_mechanisms" ; - treatment:prompt.separator "*" ; - rdfs:range treatment:TreatmentMechanism ; - skos:definition "semicolon-separated list of treatment to asterisk-separated mechanism associations" . - -treatment:treatments a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "treatments" ; - treatment:prompt.examples "Imatinib, exercise, surgery" ; - rdfs:range treatment:Treatment ; - skos:definition "semicolon-separated list of therapies and treatments are indicated for treating the disease." . - -<http://example.org/UNKNOWN/rdfs/label> a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "label" ; - treatment:owl "AnnotationProperty, AnnotationAssertion" ; - rdfs:range linkml:String ; - skos:altLabel "name" ; - skos:definition "The label (name) of the named thing" ; - skos:exactMatch <http://example.org/UNKNOWN/rdfs/label> . - -<http://purl.obolibrary.org/obo/NCIT_C149701> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "UNSPECIFIED_METHOD_OF_ADMINISTRATION" . - -<http://purl.obolibrary.org/obo/NCIT_C18902> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_APPLICABLE" . - -<http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> a <http://w3id.org/ontogpt/core/NullDataOptions>, - owl:Class ; - rdfs:label "NOT_MENTIONED" . - -<http://w3id.org/ontogpt/core/RelationshipType> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "RelationshipType" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/Triple> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Triple" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/RelationshipType> ; - owl:onProperty <http://w3id.org/ontogpt/core/predicate> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/object_qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/qualifier> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass <http://w3id.org/ontogpt/core/NamedEntity> ; - owl:onProperty <http://w3id.org/ontogpt/core/subject_qualifier> ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - skos:definition "Abstract parent for Relation Extraction tasks" ; - linkml:attributes "{'subject': SlotDefinition(name='subject', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'predicate': SlotDefinition(name='predicate', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='RelationshipType', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object': SlotDefinition(name='object', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'qualifier': SlotDefinition(name='qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A qualifier for the statements, e.g. \"NOT\" for negation', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'subject_qualifier': SlotDefinition(name='subject_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'object_qualifier': SlotDefinition(name='object_qualifier', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='NamedEntity', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/id> a owl:ObjectProperty, - linkml:SlotDefinition . - -treatment:AdverseEffect a owl:Class, - linkml:ClassDefinition ; - rdfs:label "AdverseEffect" ; - treatment:annotators "sqlite:obo:hp, sqlite:obo:ncit" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -treatment:Disease a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Disease" ; - treatment:annotators "sqlite:obo:mondo" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -treatment:Drug a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Drug" ; - treatment:annotators "sqlite:obo:chebi, sqlite:obo:drugbank" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -treatment:Mechanism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Mechanism" ; - treatment:annotators "sqlite:obo:go, sqlite:obo:ncit, sqlite:obo:mesh" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -treatment:TreatmentAdverseEffect a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TreatmentAdverseEffect" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass treatment:Treatment ; - owl:onProperty treatment:treatment ], - [ a owl:Restriction ; - owl:allValuesFrom treatment:AdverseEffect ; - owl:onProperty treatment:adverse_effects ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'adverse_effects': SlotDefinition(name='adverse_effects', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=True, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='AdverseEffect', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -treatment:TreatmentEfficacy a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TreatmentEfficacy" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass treatment:Treatment ; - owl:onProperty treatment:treatment ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty treatment:efficacy ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'efficacy': SlotDefinition(name='efficacy', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -treatment:TreatmentMechanism a owl:Class, - linkml:ClassDefinition ; - rdfs:label "TreatmentMechanism" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass treatment:Mechanism ; - owl:onProperty treatment:mechanism ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass treatment:Treatment ; - owl:onProperty treatment:treatment ], - <http://w3id.org/ontogpt/core/CompoundExpression> ; - linkml:attributes "{'treatment': SlotDefinition(name='treatment', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Treatment', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'mechanism': SlotDefinition(name='mechanism', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='Mechanism', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" ; - linkml:is_a "CompoundExpression" . - -<http://w3id.org/ontogpt/core/NullDataOptions> a owl:Class, - linkml:EnumDefinition ; - rdfs:label "NullDataOptions" ; - owl:unionOf ( <http://purl.obolibrary.org/obo/NCIT_C149701> <http://purl.obolibrary.org/obo/NCIT_C18902> <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> ) ; - linkml:permissible_values <http://purl.obolibrary.org/obo/NCIT_C149701>, - <http://purl.obolibrary.org/obo/NCIT_C18902>, - <http://w3id.org/ontogpt/core/NullDataOptions#NOT_MENTIONED> . - -<http://w3id.org/ontogpt/core/Publication> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Publication" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/combined_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/title> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/full_text> ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/abstract> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The publication identifier', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'title': SlotDefinition(name='title', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The title of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'abstract': SlotDefinition(name='abstract', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The abstract of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'combined_text': SlotDefinition(name='combined_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'full_text': SlotDefinition(name='full_text', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The full text of the publication', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -treatment:treatment a owl:ObjectProperty, - linkml:SlotDefinition . - -<http://w3id.org/ontogpt/core/Any> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Any" ; - skos:exactMatch linkml:Any ; - linkml:attributes "{}" . - -<http://w3id.org/ontogpt/core/CompoundExpression> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "CompoundExpression" ; - linkml:attributes "{}" . - -treatment:Treatment a owl:Class, - linkml:ClassDefinition ; - rdfs:label "Treatment" ; - treatment:annotators "sqlite:obo:maxo, sqlite:obo:ncit, sqlite:obo:mesh, sqlite:obo:chebi" ; - rdfs:subClassOf <http://w3id.org/ontogpt/core/NamedEntity> ; - linkml:attributes "{}" ; - linkml:is_a "NamedEntity" . - -<http://w3id.org/ontogpt/core/NamedEntity> a owl:Class, - linkml:ClassDefinition ; - rdfs:label "NamedEntity" ; - rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty <http://w3id.org/ontogpt/core/id> ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty <http://example.org/UNKNOWN/rdfs/label> ] ; - linkml:attributes "{'id': SlotDefinition(name='id', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'prompt.skip': Annotation(tag='prompt.skip', value='true', extensions={}, annotations={})}, description='A unique identifier for the named entity', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['this is populated during the grounding and normalization step'], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=True, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'label': SlotDefinition(name='label', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={'owl': Annotation(tag='owl', value='AnnotationProperty, AnnotationAssertion', extensions={}, annotations={})}, description='The label (name) of the named thing', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=['name'], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri='rdfs:label', multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range='string', range_expression=None, enum_range=None, required=None, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . - -linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "class_expression" . - -linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" ; - linkml:attributes "{}" ; - linkml:is_a "definition" ; - linkml:mixins "slot_expression" . - - diff --git a/projects/treatment/prefixmap/treatment.yaml b/projects/treatment/prefixmap/treatment.yaml deleted file mode 100644 index c0137da11..000000000 --- a/projects/treatment/prefixmap/treatment.yaml +++ /dev/null @@ -1,37 +0,0 @@ -{ - "HGNC": "http://example.org/UNKNOWN/HGNC/", - "HP": "http://example.org/UNKNOWN/HP/", - "RO": "http://purl.obolibrary.org/obo/RO_", - "biolink": "http://example.org/UNKNOWN/biolink/", - "core": "http://w3id.org/ontogpt/core/", - "linkml": "https://w3id.org/linkml/", - "rdfs": "http://example.org/UNKNOWN/rdfs/", - "treatment": "http://w3id.org/ontogpt/treatments/", - "AnnotatorResult": { - "@id": "core:AnnotatorResult" - }, - "Any": { - "@id": "linkml:Any" - }, - "CompoundExpression": { - "@id": "core:CompoundExpression" - }, - "ExtractionResult": { - "@id": "core:ExtractionResult" - }, - "NamedEntity": { - "@id": "core:NamedEntity" - }, - "Publication": { - "@id": "core:Publication" - }, - "RelationshipType": { - "@id": "core:RelationshipType" - }, - "TextWithTriples": { - "@id": "core:TextWithTriples" - }, - "Triple": { - "@id": "core:Triple" - } -} diff --git a/projects/treatment/protobuf/treatment.proto b/projects/treatment/protobuf/treatment.proto deleted file mode 100644 index f6abf4613..000000000 --- a/projects/treatment/protobuf/treatment.proto +++ /dev/null @@ -1,95 +0,0 @@ -message AdverseEffect - { - string id = 0 - string label = 0 - } -message AnnotatorResult - { - string subjectText = 0 - string objectId = 0 - string objectText = 0 - } -message Disease - { - string id = 0 - string label = 0 - } -message DiseaseTreatmentSummary - { - disease disease = 0 - repeated drug drugs = 0 - repeated treatment treatments = 0 - repeated treatment contraindications = 0 - repeated treatmentMechanism treatmentMechanisms = 0 - repeated treatmentEfficacy treatmentEfficacies = 0 - repeated treatmentAdverseEffect treatmentAdverseEffects = 0 - } -message Drug - { - string id = 0 - string label = 0 - } -// A result of extracting knowledge on text -message ExtractionResult - { - string inputId = 0 - string inputTitle = 0 - string inputText = 0 - string rawCompletionOutput = 0 - string prompt = 0 - any extractedObject = 0 - repeated any namedEntities = 0 - } -message Gene - { - string id = 0 - string label = 0 - } -message Mechanism - { - string id = 0 - string label = 0 - } -message Publication - { - string id = 0 - string title = 0 - string abstract = 0 - string combinedText = 0 - string fullText = 0 - } -message RelationshipType - { - string id = 0 - string label = 0 - } -message Symptom - { - string id = 0 - string label = 0 - } -message TextWithTriples - { - publication publication = 0 - repeated triple triples = 0 - } -message Treatment - { - string id = 0 - string label = 0 - } -message TreatmentAdverseEffect - { - treatment treatment = 0 - repeated adverseEffect adverseEffects = 0 - } -message TreatmentEfficacy - { - treatment treatment = 0 - string efficacy = 0 - } -message TreatmentMechanism - { - treatment treatment = 0 - mechanism mechanism = 0 - } diff --git a/projects/treatment/shacl/treatment.shacl.ttl b/projects/treatment/shacl/treatment.shacl.ttl deleted file mode 100644 index db93ed7d9..000000000 --- a/projects/treatment/shacl/treatment.shacl.ttl +++ /dev/null @@ -1,345 +0,0 @@ -@prefix linkml: <https://w3id.org/linkml/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix sh: <http://www.w3.org/ns/shacl#> . -@prefix treatment: <http://w3id.org/ontogpt/treatments/> . -@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . - -<http://w3id.org/ontogpt/core/AnnotatorResult> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object_text> ], - [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/object_id> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject_text> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/AnnotatorResult> . - -<http://w3id.org/ontogpt/core/CompoundExpression> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass <http://w3id.org/ontogpt/core/CompoundExpression> . - -<http://w3id.org/ontogpt/core/ExtractionResult> a sh:NodeShape ; - sh:closed true ; - sh:description "A result of extracting knowledge on text" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/input_title> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/raw_completion_output> ], - [ sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/input_id> ], - [ sh:class linkml:Any ; - sh:description "Named entities extracted from the text" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path <http://w3id.org/ontogpt/core/named_entities> ], - [ sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/input_text> ], - [ sh:class linkml:Any ; - sh:description "The complex objects extracted from the text" ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/extracted_object> ], - [ sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/prompt> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/ExtractionResult> . - -<http://w3id.org/ontogpt/core/TextWithTriples> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/Triple> ; - sh:nodeKind sh:BlankNode ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/triples> ], - [ sh:class <http://w3id.org/ontogpt/core/Publication> ; - sh:maxCount 1 ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/publication> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/TextWithTriples> . - -treatment:DiseaseTreatmentSummary a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class treatment:TreatmentMechanism ; - sh:description "semicolon-separated list of treatment to asterisk-separated mechanism associations" ; - sh:nodeKind sh:BlankNode ; - sh:order 4 ; - sh:path treatment:treatment_mechanisms ], - [ sh:class treatment:Disease ; - sh:description "the name of the disease that is treated." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path treatment:disease ], - [ sh:class treatment:TreatmentEfficacy ; - sh:description "semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective" ; - sh:nodeKind sh:BlankNode ; - sh:order 5 ; - sh:path treatment:treatment_efficacies ], - [ sh:class treatment:Drug ; - sh:description "semicolon-separated list of named small molecule drugs" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path treatment:drugs ], - [ sh:class treatment:Treatment ; - sh:description "semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path treatment:contraindications ], - [ sh:class treatment:Treatment ; - sh:description "semicolon-separated list of therapies and treatments are indicated for treating the disease." ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path treatment:treatments ], - [ sh:class treatment:TreatmentAdverseEffect ; - sh:description "semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea" ; - sh:nodeKind sh:BlankNode ; - sh:order 6 ; - sh:path treatment:treatment_adverse_effects ] ; - sh:targetClass treatment:DiseaseTreatmentSummary . - -treatment:Gene a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass treatment:Gene . - -treatment:Symptom a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass treatment:Symptom . - -<http://w3id.org/ontogpt/core/Publication> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The title of the publication" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/title> ], - [ sh:description "The publication identifier" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The full text of the publication" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/full_text> ], - [ sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/combined_text> ], - [ sh:description "The abstract of the publication" ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/abstract> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Publication> . - -<http://w3id.org/ontogpt/core/RelationshipType> a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/RelationshipType> . - -<http://w3id.org/ontogpt/core/Triple> a sh:NodeShape ; - sh:closed false ; - sh:description "Abstract parent for Relation Extraction tasks" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path <http://w3id.org/ontogpt/core/object> ], - [ sh:class <http://w3id.org/ontogpt/core/RelationshipType> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path <http://w3id.org/ontogpt/core/predicate> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path <http://w3id.org/ontogpt/core/object_qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:description "An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path <http://w3id.org/ontogpt/core/subject_qualifier> ], - [ sh:description "A qualifier for the statements, e.g. \"NOT\" for negation" ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path <http://w3id.org/ontogpt/core/qualifier> ], - [ sh:class <http://w3id.org/ontogpt/core/NamedEntity> ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/subject> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/Triple> . - -treatment:AdverseEffect a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass treatment:AdverseEffect . - -treatment:Disease a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass treatment:Disease . - -treatment:Drug a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass treatment:Drug . - -treatment:Mechanism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass treatment:Mechanism . - -treatment:TreatmentAdverseEffect a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class treatment:Treatment ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path treatment:treatment ], - [ sh:class treatment:AdverseEffect ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path treatment:adverse_effects ] ; - sh:targetClass treatment:TreatmentAdverseEffect . - -treatment:TreatmentEfficacy a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:maxCount 1 ; - sh:order 1 ; - sh:path treatment:efficacy ], - [ sh:class treatment:Treatment ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path treatment:treatment ] ; - sh:targetClass treatment:TreatmentEfficacy . - -treatment:TreatmentMechanism a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class treatment:Treatment ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path treatment:treatment ], - [ sh:class treatment:Mechanism ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path treatment:mechanism ] ; - sh:targetClass treatment:TreatmentMechanism . - -linkml:Any a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:targetClass linkml:Any . - -<http://w3id.org/ontogpt/core/NamedEntity> a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ], - [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ] ; - sh:targetClass <http://w3id.org/ontogpt/core/NamedEntity> . - -treatment:Treatment a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A unique identifier for the named entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path <http://w3id.org/ontogpt/core/id> ], - [ sh:description "The label (name) of the named thing" ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path <rdfs:label> ] ; - sh:targetClass treatment:Treatment . - diff --git a/projects/treatment/shex/treatment.shex b/projects/treatment/shex/treatment.shex deleted file mode 100644 index 894306fd7..000000000 --- a/projects/treatment/shex/treatment.shex +++ /dev/null @@ -1,235 +0,0 @@ -BASE <http://w3id.org/ontogpt/treatments/> -PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> -PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> -PREFIX linkml: <https://w3id.org/linkml/> -PREFIX core: <http://w3id.org/ontogpt/core/> -PREFIX rdfs1: <http://example.org/UNKNOWN/rdfs/> - - -linkml:String xsd:string - -linkml:Integer xsd:integer - -linkml:Boolean xsd:boolean - -linkml:Float xsd:float - -linkml:Double xsd:double - -linkml:Decimal xsd:decimal - -linkml:Time xsd:time - -linkml:Date xsd:date - -linkml:Datetime xsd:dateTime - -linkml:DateOrDatetime linkml:DateOrDatetime - -linkml:Uriorcurie IRI - -linkml:Curie xsd:string - -linkml:Uri IRI - -linkml:Ncname xsd:string - -linkml:Objectidentifier IRI - -linkml:Nodeidentifier NONLITERAL - -linkml:Jsonpointer xsd:string - -linkml:Jsonpath xsd:string - -linkml:Sparqlpath xsd:string - -<AdverseEffect> CLOSED { - ( $<AdverseEffect_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <AdverseEffect> ] - ) -} - -core:AnnotatorResult CLOSED { - ( $core:AnnotatorResult_tes ( core:subject_text @linkml:String ? ; - core:object_id @linkml:String ? ; - core:object_text @linkml:String ? - ) ; - rdf:type [ core:AnnotatorResult ] ? - ) -} - -core:Any CLOSED { - ( $core:Any_tes rdf:type . * ; - rdf:type [ linkml:Any ] ? - ) -} - -core:CompoundExpression ( - @<TreatmentAdverseEffect> OR @<TreatmentEfficacy> OR @<TreatmentMechanism> OR @core:Triple -) - -core:CompoundExpression_struct { - ( $core:CompoundExpression_tes rdf:type . * ; - rdf:type [ core:CompoundExpression ] ? - ) -} - -<Disease> CLOSED { - ( $<Disease_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Disease> ] - ) -} - -<DiseaseTreatmentSummary> CLOSED { - ( $<DiseaseTreatmentSummary_tes> ( <disease> @<Disease> ? ; - <drugs> @<Drug> * ; - <treatments> @<Treatment> * ; - <contraindications> @<Treatment> * ; - <treatment_mechanisms> @<TreatmentMechanism> * ; - <treatment_efficacies> @<TreatmentEfficacy> * ; - <treatment_adverse_effects> @<TreatmentAdverseEffect> * - ) ; - rdf:type [ <DiseaseTreatmentSummary> ] ? - ) -} - -<Drug> CLOSED { - ( $<Drug_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Drug> ] - ) -} - -core:ExtractionResult CLOSED { - ( $core:ExtractionResult_tes ( core:input_id @linkml:String ? ; - core:input_title @linkml:String ? ; - core:input_text @linkml:String ? ; - core:raw_completion_output @linkml:String ? ; - core:prompt @linkml:String ? ; - core:extracted_object @core:Any ? ; - core:named_entities @core:Any * - ) ; - rdf:type [ core:ExtractionResult ] ? - ) -} - -<Gene> CLOSED { - ( $<Gene_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Gene> ] - ) -} - -<Mechanism> CLOSED { - ( $<Mechanism_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Mechanism> ] - ) -} - -core:NamedEntity ( - @<AdverseEffect> OR @<Disease> OR @<Drug> OR @<Gene> OR @<Mechanism> OR @core:RelationshipType OR @<Symptom> OR @<Treatment> -) - -core:NamedEntity_struct { - ( $core:NamedEntity_tes rdfs1:label @linkml:String ? ; - rdf:type [ core:NamedEntity ] - ) -} - -core:Publication CLOSED { - ( $core:Publication_tes ( core:id @linkml:String ? ; - core:title @linkml:String ? ; - core:abstract @linkml:String ? ; - core:combined_text @linkml:String ? ; - core:full_text @linkml:String ? - ) ; - rdf:type [ core:Publication ] ? - ) -} - -core:RelationshipType CLOSED { - ( $core:RelationshipType_tes ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ core:RelationshipType ] - ) -} - -<Symptom> CLOSED { - ( $<Symptom_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Symptom> ] - ) -} - -core:TextWithTriples CLOSED { - ( $core:TextWithTriples_tes ( core:publication @core:Publication ? ; - core:triples @core:Triple * - ) ; - rdf:type [ core:TextWithTriples ] ? - ) -} - -<Treatment> CLOSED { - ( $<Treatment_tes> ( &core:NamedEntity_tes ; - rdf:type [ core:NamedEntity ] ? - ) ; - rdf:type [ <Treatment> ] - ) -} - -<TreatmentAdverseEffect> CLOSED { - ( $<TreatmentAdverseEffect_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <treatment> @<Treatment> ? ; - <adverse_effects> @<AdverseEffect> * - ) ; - rdf:type [ <TreatmentAdverseEffect> ] ? - ) -} - -<TreatmentEfficacy> CLOSED { - ( $<TreatmentEfficacy_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <treatment> @<Treatment> ? ; - <efficacy> @linkml:String ? - ) ; - rdf:type [ <TreatmentEfficacy> ] ? - ) -} - -<TreatmentMechanism> CLOSED { - ( $<TreatmentMechanism_tes> ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - <treatment> @<Treatment> ? ; - <mechanism> @<Mechanism> ? - ) ; - rdf:type [ <TreatmentMechanism> ] ? - ) -} - -core:Triple { - ( $core:Triple_tes ( &core:CompoundExpression_tes ; - rdf:type [ core:CompoundExpression ] ? ; - core:subject @core:NamedEntity ? ; - core:predicate @core:RelationshipType ? ; - core:object @core:NamedEntity ? ; - core:qualifier @linkml:String ? ; - core:subject_qualifier @core:NamedEntity ? ; - core:object_qualifier @core:NamedEntity ? - ) ; - rdf:type [ core:Triple ] ? - ) -} - - diff --git a/projects/treatment/sqlschema/treatment.sql b/projects/treatment/sqlschema/treatment.sql deleted file mode 100644 index ab4c20588..000000000 --- a/projects/treatment/sqlschema/treatment.sql +++ /dev/null @@ -1,116 +0,0 @@ - - -CREATE TABLE "AdverseEffect" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "AnnotatorResult" ( - subject_text TEXT, - object_id TEXT, - object_text TEXT, - PRIMARY KEY (subject_text, object_id, object_text) -); - -CREATE TABLE "Disease" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Drug" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "ExtractionResult" ( - input_id TEXT, - input_title TEXT, - input_text TEXT, - raw_completion_output TEXT, - prompt TEXT, - extracted_object TEXT, - named_entities TEXT, - PRIMARY KEY (input_id, input_title, input_text, raw_completion_output, prompt, extracted_object, named_entities) -); - -CREATE TABLE "Gene" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Mechanism" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Publication" ( - id TEXT, - title TEXT, - abstract TEXT, - combined_text TEXT, - full_text TEXT, - PRIMARY KEY (id, title, abstract, combined_text, full_text) -); - -CREATE TABLE "RelationshipType" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "Symptom" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "TextWithTriples" ( - publication TEXT, - triples TEXT, - PRIMARY KEY (publication, triples) -); - -CREATE TABLE "Treatment" ( - id TEXT NOT NULL, - label TEXT, - PRIMARY KEY (id) -); - -CREATE TABLE "DiseaseTreatmentSummary" ( - disease TEXT, - drugs TEXT, - treatments TEXT, - contraindications TEXT, - treatment_mechanisms TEXT, - treatment_efficacies TEXT, - treatment_adverse_effects TEXT, - PRIMARY KEY (disease, drugs, treatments, contraindications, treatment_mechanisms, treatment_efficacies, treatment_adverse_effects), - FOREIGN KEY(disease) REFERENCES "Disease" (id) -); - -CREATE TABLE "TreatmentAdverseEffect" ( - treatment TEXT, - adverse_effects TEXT, - PRIMARY KEY (treatment, adverse_effects), - FOREIGN KEY(treatment) REFERENCES "Treatment" (id) -); - -CREATE TABLE "TreatmentEfficacy" ( - treatment TEXT, - efficacy TEXT, - PRIMARY KEY (treatment, efficacy), - FOREIGN KEY(treatment) REFERENCES "Treatment" (id) -); - -CREATE TABLE "TreatmentMechanism" ( - treatment TEXT, - mechanism TEXT, - PRIMARY KEY (treatment, mechanism), - FOREIGN KEY(treatment) REFERENCES "Treatment" (id), - FOREIGN KEY(mechanism) REFERENCES "Mechanism" (id) -); diff --git a/projects/treatment/treatment.py b/projects/treatment/treatment.py deleted file mode 100644 index 03f70ef31..000000000 --- a/projects/treatment/treatment.py +++ /dev/null @@ -1,722 +0,0 @@ -# Auto generated from treatment.yaml by pythongen.py version: 0.9.0 -# Generation date: 2023-08-07T10:56:46 -# Schema: treatment-template -# -# id: http://w3id.org/ontogpt/treatment -# description: A template for MAXO treatments -# license: https://creativecommons.org/publicdomain/zero/1.0/ - -import dataclasses -import sys -import re -from jsonasobj2 import JsonObj, as_dict -from typing import Optional, List, Union, Dict, ClassVar, Any -from dataclasses import dataclass -from linkml_runtime.linkml_model.meta import EnumDefinition, PermissibleValue, PvFormulaOptions - -from linkml_runtime.utils.slot import Slot -from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode -from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int -from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs -from linkml_runtime.utils.formatutils import camelcase, underscore, sfx -from linkml_runtime.utils.enumerations import EnumDefinitionImpl -from rdflib import Namespace, URIRef -from linkml_runtime.utils.curienamespace import CurieNamespace -from linkml_runtime.linkml_model.types import String - -metamodel_version = "1.7.0" -version = None - -# Overwrite dataclasses _init_fn to add **kwargs in __init__ -dataclasses._init_fn = dataclasses_init_fn_with_kwargs - -# Namespaces -HGNC = CurieNamespace('HGNC', 'http://example.org/UNKNOWN/HGNC/') -HP = CurieNamespace('HP', 'http://example.org/UNKNOWN/HP/') -RO = CurieNamespace('RO', 'http://purl.obolibrary.org/obo/RO_') -BIOLINK = CurieNamespace('biolink', 'http://example.org/UNKNOWN/biolink/') -CORE = CurieNamespace('core', 'http://w3id.org/ontogpt/core/') -LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') -RDFS = CurieNamespace('rdfs', 'http://example.org/UNKNOWN/rdfs/') -TREATMENT = CurieNamespace('treatment', 'http://w3id.org/ontogpt/treatments/') -DEFAULT_ = TREATMENT - - -# Types - -# Class references -class NamedEntityId(extended_str): - pass - - -class GeneId(NamedEntityId): - pass - - -class SymptomId(NamedEntityId): - pass - - -class DiseaseId(NamedEntityId): - pass - - -class AdverseEffectId(NamedEntityId): - pass - - -class TreatmentId(NamedEntityId): - pass - - -class MechanismId(NamedEntityId): - pass - - -class DrugId(NamedEntityId): - pass - - -class RelationshipTypeId(NamedEntityId): - pass - - -@dataclass -class DiseaseTreatmentSummary(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.DiseaseTreatmentSummary - class_class_curie: ClassVar[str] = "treatment:DiseaseTreatmentSummary" - class_name: ClassVar[str] = "DiseaseTreatmentSummary" - class_model_uri: ClassVar[URIRef] = TREATMENT.DiseaseTreatmentSummary - - disease: Optional[Union[str, DiseaseId]] = None - drugs: Optional[Union[Union[str, DrugId], List[Union[str, DrugId]]]] = empty_list() - treatments: Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]] = empty_list() - contraindications: Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]] = empty_list() - treatment_mechanisms: Optional[Union[Union[dict, "TreatmentMechanism"], List[Union[dict, "TreatmentMechanism"]]]] = empty_list() - treatment_efficacies: Optional[Union[Union[dict, "TreatmentEfficacy"], List[Union[dict, "TreatmentEfficacy"]]]] = empty_list() - treatment_adverse_effects: Optional[Union[Union[dict, "TreatmentAdverseEffect"], List[Union[dict, "TreatmentAdverseEffect"]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.disease is not None and not isinstance(self.disease, DiseaseId): - self.disease = DiseaseId(self.disease) - - if not isinstance(self.drugs, list): - self.drugs = [self.drugs] if self.drugs is not None else [] - self.drugs = [v if isinstance(v, DrugId) else DrugId(v) for v in self.drugs] - - if not isinstance(self.treatments, list): - self.treatments = [self.treatments] if self.treatments is not None else [] - self.treatments = [v if isinstance(v, TreatmentId) else TreatmentId(v) for v in self.treatments] - - if not isinstance(self.contraindications, list): - self.contraindications = [self.contraindications] if self.contraindications is not None else [] - self.contraindications = [v if isinstance(v, TreatmentId) else TreatmentId(v) for v in self.contraindications] - - if not isinstance(self.treatment_mechanisms, list): - self.treatment_mechanisms = [self.treatment_mechanisms] if self.treatment_mechanisms is not None else [] - self.treatment_mechanisms = [v if isinstance(v, TreatmentMechanism) else TreatmentMechanism(**as_dict(v)) for v in self.treatment_mechanisms] - - if not isinstance(self.treatment_efficacies, list): - self.treatment_efficacies = [self.treatment_efficacies] if self.treatment_efficacies is not None else [] - self.treatment_efficacies = [v if isinstance(v, TreatmentEfficacy) else TreatmentEfficacy(**as_dict(v)) for v in self.treatment_efficacies] - - if not isinstance(self.treatment_adverse_effects, list): - self.treatment_adverse_effects = [self.treatment_adverse_effects] if self.treatment_adverse_effects is not None else [] - self.treatment_adverse_effects = [v if isinstance(v, TreatmentAdverseEffect) else TreatmentAdverseEffect(**as_dict(v)) for v in self.treatment_adverse_effects] - - super().__post_init__(**kwargs) - - -Any = Any - -@dataclass -class ExtractionResult(YAMLRoot): - """ - A result of extracting knowledge on text - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.ExtractionResult - class_class_curie: ClassVar[str] = "core:ExtractionResult" - class_name: ClassVar[str] = "ExtractionResult" - class_model_uri: ClassVar[URIRef] = TREATMENT.ExtractionResult - - input_id: Optional[str] = None - input_title: Optional[str] = None - input_text: Optional[str] = None - raw_completion_output: Optional[str] = None - prompt: Optional[str] = None - extracted_object: Optional[Union[dict, Any]] = None - named_entities: Optional[Union[Union[dict, Any], List[Union[dict, Any]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.input_id is not None and not isinstance(self.input_id, str): - self.input_id = str(self.input_id) - - if self.input_title is not None and not isinstance(self.input_title, str): - self.input_title = str(self.input_title) - - if self.input_text is not None and not isinstance(self.input_text, str): - self.input_text = str(self.input_text) - - if self.raw_completion_output is not None and not isinstance(self.raw_completion_output, str): - self.raw_completion_output = str(self.raw_completion_output) - - if self.prompt is not None and not isinstance(self.prompt, str): - self.prompt = str(self.prompt) - - super().__post_init__(**kwargs) - - -@dataclass -class NamedEntity(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.NamedEntity - class_class_curie: ClassVar[str] = "core:NamedEntity" - class_name: ClassVar[str] = "NamedEntity" - class_model_uri: ClassVar[URIRef] = TREATMENT.NamedEntity - - id: Union[str, NamedEntityId] = None - label: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, NamedEntityId): - self.id = NamedEntityId(self.id) - - if self.label is not None and not isinstance(self.label, str): - self.label = str(self.label) - - super().__post_init__(**kwargs) - - -@dataclass -class Gene(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.Gene - class_class_curie: ClassVar[str] = "treatment:Gene" - class_name: ClassVar[str] = "Gene" - class_model_uri: ClassVar[URIRef] = TREATMENT.Gene - - id: Union[str, GeneId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, GeneId): - self.id = GeneId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Symptom(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.Symptom - class_class_curie: ClassVar[str] = "treatment:Symptom" - class_name: ClassVar[str] = "Symptom" - class_model_uri: ClassVar[URIRef] = TREATMENT.Symptom - - id: Union[str, SymptomId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, SymptomId): - self.id = SymptomId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Disease(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.Disease - class_class_curie: ClassVar[str] = "treatment:Disease" - class_name: ClassVar[str] = "Disease" - class_model_uri: ClassVar[URIRef] = TREATMENT.Disease - - id: Union[str, DiseaseId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DiseaseId): - self.id = DiseaseId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class AdverseEffect(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.AdverseEffect - class_class_curie: ClassVar[str] = "treatment:AdverseEffect" - class_name: ClassVar[str] = "AdverseEffect" - class_model_uri: ClassVar[URIRef] = TREATMENT.AdverseEffect - - id: Union[str, AdverseEffectId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, AdverseEffectId): - self.id = AdverseEffectId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Treatment(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.Treatment - class_class_curie: ClassVar[str] = "treatment:Treatment" - class_name: ClassVar[str] = "Treatment" - class_model_uri: ClassVar[URIRef] = TREATMENT.Treatment - - id: Union[str, TreatmentId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, TreatmentId): - self.id = TreatmentId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Mechanism(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.Mechanism - class_class_curie: ClassVar[str] = "treatment:Mechanism" - class_name: ClassVar[str] = "Mechanism" - class_model_uri: ClassVar[URIRef] = TREATMENT.Mechanism - - id: Union[str, MechanismId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, MechanismId): - self.id = MechanismId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Drug(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.Drug - class_class_curie: ClassVar[str] = "treatment:Drug" - class_name: ClassVar[str] = "Drug" - class_model_uri: ClassVar[URIRef] = TREATMENT.Drug - - id: Union[str, DrugId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, DrugId): - self.id = DrugId(self.id) - - super().__post_init__(**kwargs) - - -class CompoundExpression(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.CompoundExpression - class_class_curie: ClassVar[str] = "core:CompoundExpression" - class_name: ClassVar[str] = "CompoundExpression" - class_model_uri: ClassVar[URIRef] = TREATMENT.CompoundExpression - - -@dataclass -class TreatmentMechanism(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.TreatmentMechanism - class_class_curie: ClassVar[str] = "treatment:TreatmentMechanism" - class_name: ClassVar[str] = "TreatmentMechanism" - class_model_uri: ClassVar[URIRef] = TREATMENT.TreatmentMechanism - - treatment: Optional[Union[str, TreatmentId]] = None - mechanism: Optional[Union[str, MechanismId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.treatment is not None and not isinstance(self.treatment, TreatmentId): - self.treatment = TreatmentId(self.treatment) - - if self.mechanism is not None and not isinstance(self.mechanism, MechanismId): - self.mechanism = MechanismId(self.mechanism) - - super().__post_init__(**kwargs) - - -@dataclass -class TreatmentAdverseEffect(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.TreatmentAdverseEffect - class_class_curie: ClassVar[str] = "treatment:TreatmentAdverseEffect" - class_name: ClassVar[str] = "TreatmentAdverseEffect" - class_model_uri: ClassVar[URIRef] = TREATMENT.TreatmentAdverseEffect - - treatment: Optional[Union[str, TreatmentId]] = None - adverse_effects: Optional[Union[Union[str, AdverseEffectId], List[Union[str, AdverseEffectId]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.treatment is not None and not isinstance(self.treatment, TreatmentId): - self.treatment = TreatmentId(self.treatment) - - if not isinstance(self.adverse_effects, list): - self.adverse_effects = [self.adverse_effects] if self.adverse_effects is not None else [] - self.adverse_effects = [v if isinstance(v, AdverseEffectId) else AdverseEffectId(v) for v in self.adverse_effects] - - super().__post_init__(**kwargs) - - -@dataclass -class TreatmentEfficacy(CompoundExpression): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = TREATMENT.TreatmentEfficacy - class_class_curie: ClassVar[str] = "treatment:TreatmentEfficacy" - class_name: ClassVar[str] = "TreatmentEfficacy" - class_model_uri: ClassVar[URIRef] = TREATMENT.TreatmentEfficacy - - treatment: Optional[Union[str, TreatmentId]] = None - efficacy: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.treatment is not None and not isinstance(self.treatment, TreatmentId): - self.treatment = TreatmentId(self.treatment) - - if self.efficacy is not None and not isinstance(self.efficacy, str): - self.efficacy = str(self.efficacy) - - super().__post_init__(**kwargs) - - -@dataclass -class Triple(CompoundExpression): - """ - Abstract parent for Relation Extraction tasks - """ - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Triple - class_class_curie: ClassVar[str] = "core:Triple" - class_name: ClassVar[str] = "Triple" - class_model_uri: ClassVar[URIRef] = TREATMENT.Triple - - subject: Optional[Union[str, NamedEntityId]] = None - predicate: Optional[Union[str, RelationshipTypeId]] = None - object: Optional[Union[str, NamedEntityId]] = None - qualifier: Optional[str] = None - subject_qualifier: Optional[Union[str, NamedEntityId]] = None - object_qualifier: Optional[Union[str, NamedEntityId]] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject is not None and not isinstance(self.subject, NamedEntityId): - self.subject = NamedEntityId(self.subject) - - if self.predicate is not None and not isinstance(self.predicate, RelationshipTypeId): - self.predicate = RelationshipTypeId(self.predicate) - - if self.object is not None and not isinstance(self.object, NamedEntityId): - self.object = NamedEntityId(self.object) - - if self.qualifier is not None and not isinstance(self.qualifier, str): - self.qualifier = str(self.qualifier) - - if self.subject_qualifier is not None and not isinstance(self.subject_qualifier, NamedEntityId): - self.subject_qualifier = NamedEntityId(self.subject_qualifier) - - if self.object_qualifier is not None and not isinstance(self.object_qualifier, NamedEntityId): - self.object_qualifier = NamedEntityId(self.object_qualifier) - - super().__post_init__(**kwargs) - - -@dataclass -class TextWithTriples(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.TextWithTriples - class_class_curie: ClassVar[str] = "core:TextWithTriples" - class_name: ClassVar[str] = "TextWithTriples" - class_model_uri: ClassVar[URIRef] = TREATMENT.TextWithTriples - - publication: Optional[Union[dict, "Publication"]] = None - triples: Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]] = empty_list() - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.publication is not None and not isinstance(self.publication, Publication): - self.publication = Publication(**as_dict(self.publication)) - - if not isinstance(self.triples, list): - self.triples = [self.triples] if self.triples is not None else [] - self.triples = [v if isinstance(v, Triple) else Triple(**as_dict(v)) for v in self.triples] - - super().__post_init__(**kwargs) - - -@dataclass -class RelationshipType(NamedEntity): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.RelationshipType - class_class_curie: ClassVar[str] = "core:RelationshipType" - class_name: ClassVar[str] = "RelationshipType" - class_model_uri: ClassVar[URIRef] = TREATMENT.RelationshipType - - id: Union[str, RelationshipTypeId] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self._is_empty(self.id): - self.MissingRequiredField("id") - if not isinstance(self.id, RelationshipTypeId): - self.id = RelationshipTypeId(self.id) - - super().__post_init__(**kwargs) - - -@dataclass -class Publication(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.Publication - class_class_curie: ClassVar[str] = "core:Publication" - class_name: ClassVar[str] = "Publication" - class_model_uri: ClassVar[URIRef] = TREATMENT.Publication - - id: Optional[str] = None - title: Optional[str] = None - abstract: Optional[str] = None - combined_text: Optional[str] = None - full_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.id is not None and not isinstance(self.id, str): - self.id = str(self.id) - - if self.title is not None and not isinstance(self.title, str): - self.title = str(self.title) - - if self.abstract is not None and not isinstance(self.abstract, str): - self.abstract = str(self.abstract) - - if self.combined_text is not None and not isinstance(self.combined_text, str): - self.combined_text = str(self.combined_text) - - if self.full_text is not None and not isinstance(self.full_text, str): - self.full_text = str(self.full_text) - - super().__post_init__(**kwargs) - - -@dataclass -class AnnotatorResult(YAMLRoot): - _inherited_slots: ClassVar[List[str]] = [] - - class_class_uri: ClassVar[URIRef] = CORE.AnnotatorResult - class_class_curie: ClassVar[str] = "core:AnnotatorResult" - class_name: ClassVar[str] = "AnnotatorResult" - class_model_uri: ClassVar[URIRef] = TREATMENT.AnnotatorResult - - subject_text: Optional[str] = None - object_id: Optional[str] = None - object_text: Optional[str] = None - - def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): - if self.subject_text is not None and not isinstance(self.subject_text, str): - self.subject_text = str(self.subject_text) - - if self.object_id is not None and not isinstance(self.object_id, str): - self.object_id = str(self.object_id) - - if self.object_text is not None and not isinstance(self.object_text, str): - self.object_text = str(self.object_text) - - super().__post_init__(**kwargs) - - -# Enumerations -class NCITDrugType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="NCITDrugType", - ) - -class NCITTreatmentType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="NCITTreatmentType", - ) - -class NCITTActivityType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="NCITTActivityType", - ) - -class MAXOActionType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="MAXOActionType", - ) - -class MESHTherapeuticType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="MESHTherapeuticType", - ) - -class CHEBIDrugType(EnumDefinitionImpl): - - _defn = EnumDefinition( - name="CHEBIDrugType", - ) - -class NullDataOptions(EnumDefinitionImpl): - - UNSPECIFIED_METHOD_OF_ADMINISTRATION = PermissibleValue(text="UNSPECIFIED_METHOD_OF_ADMINISTRATION", - meaning=NCIT.C149701) - NOT_APPLICABLE = PermissibleValue(text="NOT_APPLICABLE", - meaning=NCIT.C18902) - NOT_MENTIONED = PermissibleValue(text="NOT_MENTIONED") - - _defn = EnumDefinition( - name="NullDataOptions", - ) - -# Slots -class slots: - pass - -slots.diseaseTreatmentSummary__disease = Slot(uri=TREATMENT.disease, name="diseaseTreatmentSummary__disease", curie=TREATMENT.curie('disease'), - model_uri=TREATMENT.diseaseTreatmentSummary__disease, domain=None, range=Optional[Union[str, DiseaseId]]) - -slots.diseaseTreatmentSummary__drugs = Slot(uri=TREATMENT.drugs, name="diseaseTreatmentSummary__drugs", curie=TREATMENT.curie('drugs'), - model_uri=TREATMENT.diseaseTreatmentSummary__drugs, domain=None, range=Optional[Union[Union[str, DrugId], List[Union[str, DrugId]]]]) - -slots.diseaseTreatmentSummary__treatments = Slot(uri=TREATMENT.treatments, name="diseaseTreatmentSummary__treatments", curie=TREATMENT.curie('treatments'), - model_uri=TREATMENT.diseaseTreatmentSummary__treatments, domain=None, range=Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]]) - -slots.diseaseTreatmentSummary__contraindications = Slot(uri=TREATMENT.contraindications, name="diseaseTreatmentSummary__contraindications", curie=TREATMENT.curie('contraindications'), - model_uri=TREATMENT.diseaseTreatmentSummary__contraindications, domain=None, range=Optional[Union[Union[str, TreatmentId], List[Union[str, TreatmentId]]]]) - -slots.diseaseTreatmentSummary__treatment_mechanisms = Slot(uri=TREATMENT.treatment_mechanisms, name="diseaseTreatmentSummary__treatment_mechanisms", curie=TREATMENT.curie('treatment_mechanisms'), - model_uri=TREATMENT.diseaseTreatmentSummary__treatment_mechanisms, domain=None, range=Optional[Union[Union[dict, TreatmentMechanism], List[Union[dict, TreatmentMechanism]]]]) - -slots.diseaseTreatmentSummary__treatment_efficacies = Slot(uri=TREATMENT.treatment_efficacies, name="diseaseTreatmentSummary__treatment_efficacies", curie=TREATMENT.curie('treatment_efficacies'), - model_uri=TREATMENT.diseaseTreatmentSummary__treatment_efficacies, domain=None, range=Optional[Union[Union[dict, TreatmentEfficacy], List[Union[dict, TreatmentEfficacy]]]]) - -slots.diseaseTreatmentSummary__treatment_adverse_effects = Slot(uri=TREATMENT.treatment_adverse_effects, name="diseaseTreatmentSummary__treatment_adverse_effects", curie=TREATMENT.curie('treatment_adverse_effects'), - model_uri=TREATMENT.diseaseTreatmentSummary__treatment_adverse_effects, domain=None, range=Optional[Union[Union[dict, TreatmentAdverseEffect], List[Union[dict, TreatmentAdverseEffect]]]]) - -slots.treatmentMechanism__treatment = Slot(uri=TREATMENT.treatment, name="treatmentMechanism__treatment", curie=TREATMENT.curie('treatment'), - model_uri=TREATMENT.treatmentMechanism__treatment, domain=None, range=Optional[Union[str, TreatmentId]]) - -slots.treatmentMechanism__mechanism = Slot(uri=TREATMENT.mechanism, name="treatmentMechanism__mechanism", curie=TREATMENT.curie('mechanism'), - model_uri=TREATMENT.treatmentMechanism__mechanism, domain=None, range=Optional[Union[str, MechanismId]]) - -slots.treatmentAdverseEffect__treatment = Slot(uri=TREATMENT.treatment, name="treatmentAdverseEffect__treatment", curie=TREATMENT.curie('treatment'), - model_uri=TREATMENT.treatmentAdverseEffect__treatment, domain=None, range=Optional[Union[str, TreatmentId]]) - -slots.treatmentAdverseEffect__adverse_effects = Slot(uri=TREATMENT.adverse_effects, name="treatmentAdverseEffect__adverse_effects", curie=TREATMENT.curie('adverse_effects'), - model_uri=TREATMENT.treatmentAdverseEffect__adverse_effects, domain=None, range=Optional[Union[Union[str, AdverseEffectId], List[Union[str, AdverseEffectId]]]]) - -slots.treatmentEfficacy__treatment = Slot(uri=TREATMENT.treatment, name="treatmentEfficacy__treatment", curie=TREATMENT.curie('treatment'), - model_uri=TREATMENT.treatmentEfficacy__treatment, domain=None, range=Optional[Union[str, TreatmentId]]) - -slots.treatmentEfficacy__efficacy = Slot(uri=TREATMENT.efficacy, name="treatmentEfficacy__efficacy", curie=TREATMENT.curie('efficacy'), - model_uri=TREATMENT.treatmentEfficacy__efficacy, domain=None, range=Optional[str]) - -slots.extractionResult__input_id = Slot(uri=CORE.input_id, name="extractionResult__input_id", curie=CORE.curie('input_id'), - model_uri=TREATMENT.extractionResult__input_id, domain=None, range=Optional[str]) - -slots.extractionResult__input_title = Slot(uri=CORE.input_title, name="extractionResult__input_title", curie=CORE.curie('input_title'), - model_uri=TREATMENT.extractionResult__input_title, domain=None, range=Optional[str]) - -slots.extractionResult__input_text = Slot(uri=CORE.input_text, name="extractionResult__input_text", curie=CORE.curie('input_text'), - model_uri=TREATMENT.extractionResult__input_text, domain=None, range=Optional[str]) - -slots.extractionResult__raw_completion_output = Slot(uri=CORE.raw_completion_output, name="extractionResult__raw_completion_output", curie=CORE.curie('raw_completion_output'), - model_uri=TREATMENT.extractionResult__raw_completion_output, domain=None, range=Optional[str]) - -slots.extractionResult__prompt = Slot(uri=CORE.prompt, name="extractionResult__prompt", curie=CORE.curie('prompt'), - model_uri=TREATMENT.extractionResult__prompt, domain=None, range=Optional[str]) - -slots.extractionResult__extracted_object = Slot(uri=CORE.extracted_object, name="extractionResult__extracted_object", curie=CORE.curie('extracted_object'), - model_uri=TREATMENT.extractionResult__extracted_object, domain=None, range=Optional[Union[dict, Any]]) - -slots.extractionResult__named_entities = Slot(uri=CORE.named_entities, name="extractionResult__named_entities", curie=CORE.curie('named_entities'), - model_uri=TREATMENT.extractionResult__named_entities, domain=None, range=Optional[Union[Union[dict, Any], List[Union[dict, Any]]]]) - -slots.namedEntity__id = Slot(uri=CORE.id, name="namedEntity__id", curie=CORE.curie('id'), - model_uri=TREATMENT.namedEntity__id, domain=None, range=URIRef) - -slots.namedEntity__label = Slot(uri=RDFS.label, name="namedEntity__label", curie=RDFS.curie('label'), - model_uri=TREATMENT.namedEntity__label, domain=None, range=Optional[str]) - -slots.triple__subject = Slot(uri=CORE.subject, name="triple__subject", curie=CORE.curie('subject'), - model_uri=TREATMENT.triple__subject, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__predicate = Slot(uri=CORE.predicate, name="triple__predicate", curie=CORE.curie('predicate'), - model_uri=TREATMENT.triple__predicate, domain=None, range=Optional[Union[str, RelationshipTypeId]]) - -slots.triple__object = Slot(uri=CORE.object, name="triple__object", curie=CORE.curie('object'), - model_uri=TREATMENT.triple__object, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__qualifier = Slot(uri=CORE.qualifier, name="triple__qualifier", curie=CORE.curie('qualifier'), - model_uri=TREATMENT.triple__qualifier, domain=None, range=Optional[str]) - -slots.triple__subject_qualifier = Slot(uri=CORE.subject_qualifier, name="triple__subject_qualifier", curie=CORE.curie('subject_qualifier'), - model_uri=TREATMENT.triple__subject_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.triple__object_qualifier = Slot(uri=CORE.object_qualifier, name="triple__object_qualifier", curie=CORE.curie('object_qualifier'), - model_uri=TREATMENT.triple__object_qualifier, domain=None, range=Optional[Union[str, NamedEntityId]]) - -slots.textWithTriples__publication = Slot(uri=CORE.publication, name="textWithTriples__publication", curie=CORE.curie('publication'), - model_uri=TREATMENT.textWithTriples__publication, domain=None, range=Optional[Union[dict, Publication]]) - -slots.textWithTriples__triples = Slot(uri=CORE.triples, name="textWithTriples__triples", curie=CORE.curie('triples'), - model_uri=TREATMENT.textWithTriples__triples, domain=None, range=Optional[Union[Union[dict, Triple], List[Union[dict, Triple]]]]) - -slots.publication__id = Slot(uri=CORE.id, name="publication__id", curie=CORE.curie('id'), - model_uri=TREATMENT.publication__id, domain=None, range=Optional[str]) - -slots.publication__title = Slot(uri=CORE.title, name="publication__title", curie=CORE.curie('title'), - model_uri=TREATMENT.publication__title, domain=None, range=Optional[str]) - -slots.publication__abstract = Slot(uri=CORE.abstract, name="publication__abstract", curie=CORE.curie('abstract'), - model_uri=TREATMENT.publication__abstract, domain=None, range=Optional[str]) - -slots.publication__combined_text = Slot(uri=CORE.combined_text, name="publication__combined_text", curie=CORE.curie('combined_text'), - model_uri=TREATMENT.publication__combined_text, domain=None, range=Optional[str]) - -slots.publication__full_text = Slot(uri=CORE.full_text, name="publication__full_text", curie=CORE.curie('full_text'), - model_uri=TREATMENT.publication__full_text, domain=None, range=Optional[str]) - -slots.annotatorResult__subject_text = Slot(uri=CORE.subject_text, name="annotatorResult__subject_text", curie=CORE.curie('subject_text'), - model_uri=TREATMENT.annotatorResult__subject_text, domain=None, range=Optional[str]) - -slots.annotatorResult__object_id = Slot(uri=CORE.object_id, name="annotatorResult__object_id", curie=CORE.curie('object_id'), - model_uri=TREATMENT.annotatorResult__object_id, domain=None, range=Optional[str]) - -slots.annotatorResult__object_text = Slot(uri=CORE.object_text, name="annotatorResult__object_text", curie=CORE.curie('object_text'), - model_uri=TREATMENT.annotatorResult__object_text, domain=None, range=Optional[str]) \ No newline at end of file From 506cf3eb5f17fbd0fd011e6a4bf7e2a4ee0a7a2e Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 10:59:13 -0400 Subject: [PATCH 10/40] Fix missing temperature arg in suggest-template --- src/ontogpt/cli.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/ontogpt/cli.py b/src/ontogpt/cli.py index 3a01df0de..0d68dd443 100644 --- a/src/ontogpt/cli.py +++ b/src/ontogpt/cli.py @@ -1921,6 +1921,7 @@ def list_models(): @output_option_txt @output_format_options @show_prompt_option +@temperature_option @api_base_option @api_version_option @model_provider_option @@ -1931,6 +1932,7 @@ def suggest_templates( output, output_format, show_prompt, + temperature, api_base, api_version, model_provider, @@ -1975,6 +1977,7 @@ def suggest_templates( output=output, output_format=output_format, show_prompt=show_prompt, + temperature=temperature, api_base=api_base, api_version=api_version, model_provider=model_provider, From 7407c70f85abf6379f8132fb05f0fce3830273ec Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 11:02:01 -0400 Subject: [PATCH 11/40] Add more description to list-templates command --- src/ontogpt/cli.py | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/ontogpt/cli.py b/src/ontogpt/cli.py index 0d68dd443..ecf049216 100644 --- a/src/ontogpt/cli.py +++ b/src/ontogpt/cli.py @@ -1837,7 +1837,17 @@ def clinical_notes( @main.command() def list_templates(): - """List the available extraction templates.""" + """List the available extraction templates. + + The following values are provided: + + ID: The ID of the template. Use this with the -t/--template option in another command. + + Name: The name of the template. + + Description: A brief description of the template. + + """ # Get the list of yaml files in the templates directory all_templates = _get_templates() From ba5da35cf3bc20e9bc244caf74d472f263eb8d0a Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 12:32:52 -0400 Subject: [PATCH 12/40] Don't restrict HALO models --- src/ontogpt/cli.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/ontogpt/cli.py b/src/ontogpt/cli.py index ecf049216..727587cf8 100644 --- a/src/ontogpt/cli.py +++ b/src/ontogpt/cli.py @@ -1762,8 +1762,6 @@ def convert_examples(input, output): @click.argument("terms", nargs=-1) def halo(model, input, context, terms, output, **kwargs): """Run HALO over inputs.""" - if model: - raise NotImplementedError("HALO not currently supported for this model.") engine = HALOEngine() engine.seed_from_file(input) From 88bd3fd5936634cedcd35814753bb13255f1204e Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 12:37:17 -0400 Subject: [PATCH 13/40] Add check for anthropic API key --- src/ontogpt/clients/llm_client.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/ontogpt/clients/llm_client.py b/src/ontogpt/clients/llm_client.py index 2ccdb3f07..87815790e 100644 --- a/src/ontogpt/clients/llm_client.py +++ b/src/ontogpt/clients/llm_client.py @@ -35,8 +35,10 @@ class LLMClient: def __post_init__(self): # Get appropriate API key for the model source # and other details if needed - if not self.api_key: + if not self.api_key and not self.custom_llm_provider: self.api_key = get_apikey_value("openai") + elif self.custom_llm_provider == "anthropic": + self.api_key = get_apikey_value("anthropic-key") else: for service in SERVICES: if self.model.startswith(service): From db6c8312c66fe82f09a251179d7b42ca9f7ac608 Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 12:48:46 -0400 Subject: [PATCH 14/40] Temp-disable dump-completions command --- src/ontogpt/cli.py | 25 ++----------------------- 1 file changed, 2 insertions(+), 23 deletions(-) diff --git a/src/ontogpt/cli.py b/src/ontogpt/cli.py index 727587cf8..40ada36d1 100644 --- a/src/ontogpt/cli.py +++ b/src/ontogpt/cli.py @@ -1700,37 +1700,16 @@ def parse(template, input): # TODO: rewrite for use with litellm's disk cache +# See https://grantjenks.com/docs/diskcache/tutorial.html @main.command() @click.option("-o", "--output", type=click.File(mode="w"), default=sys.stdout, help="Output file.") @output_format_options @model_option @click.option("-m", "match", help="Match string to use for filtering.") @click.option("-D", "database", help="Path to sqlite database.") -@api_base_option -@api_version_option -@model_provider_option def dump_completions(model, match, database, output, output_format): """Dump cached completions.""" - client = LLMClient(model=model) - - if database: - client.cache_db_path = database - if output_format == "jsonl": - writer = jsonlines.Writer(output) - for _engine, prompt, completion in client.cached_completions(match): - writer.write(dict(engine=model, prompt=prompt, completion=completion)) - elif output_format == "yaml": - for _engine, prompt, completion in client.cached_completions(match): - output.write( - dump_minimal_yaml(dict(engine=model, prompt=prompt, completion=completion)) - ) - else: - output.write("# Cached Completions:\n") - for engine, prompt, completion in client.cached_completions(match): - output.write("## Entry\n") - output.write(f"### Engine: {engine}\n") - output.write(f"### Prompt:\n\n {prompt}\n\n") - output.write(f"### Completion:\n\n {completion}\n\n") + raise NotImplementedError("This function is not implemented at this time.") @main.command() From 333b4537c3b980f6e02ea7cddff87e02dd0ca31d Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 13:05:09 -0400 Subject: [PATCH 15/40] Fix test params --- tests/integration/test_knowledge_engines/test_spires_engine.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/integration/test_knowledge_engines/test_spires_engine.py b/tests/integration/test_knowledge_engines/test_spires_engine.py index 8a0083b39..0143e804d 100644 --- a/tests/integration/test_knowledge_engines/test_spires_engine.py +++ b/tests/integration/test_knowledge_engines/test_spires_engine.py @@ -325,7 +325,7 @@ def setUp(self) -> None: self.ke = SPIRESEngine( template_details=template_details, model=MODEL, - model_source=MODEL_SOURCE, + model_provider=MODEL_SOURCE, ) def test_setup(self): From 66c29bd7262eb01d4bc628a6bbcc67250cdacf10 Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 13:08:01 -0400 Subject: [PATCH 16/40] Move get_section_of_interest to parse_utils --- src/ontogpt/cli.py | 35 +------------------------------- src/ontogpt/utils/parse_utils.py | 35 ++++++++++++++++++++++++++++++++ 2 files changed, 36 insertions(+), 34 deletions(-) diff --git a/src/ontogpt/cli.py b/src/ontogpt/cli.py index 40ada36d1..a269ba1c2 100644 --- a/src/ontogpt/cli.py +++ b/src/ontogpt/cli.py @@ -1348,39 +1348,6 @@ def get_kanjee_prompt() -> str: return prompt -def get_section_of_interest(data, tag_of_interest): - # I blame adobe - # Find the index of the element that matches the case-insensitive regex pattern - start_index = None - pattern = re.compile(tag_of_interest, re.IGNORECASE) - if isinstance(data, str): - data = data.split("\n") - for i, item in enumerate(data): - if pattern.search(item): - start_index = i - break - - if start_index is not None: - # Find the index of the next element that starts with '<p>' - next_index = next( - ( - i - for i, item in enumerate(data[start_index + 1 :], start=start_index + 1) - if item.startswith("<p>") - ), - None, - ) - - if next_index is not None: - # Extract the desired element - result = data[next_index] - return result - else: - raise ValueError("No element starting with '<p>' found after the tag_of_interest") - else: - raise ValueError("No element matching the tag_of_interest found in the list.") - - @main.command() @inputfile_option @output_option_txt @@ -1564,7 +1531,7 @@ def fill( model_provider, **kwargs, ): - """Fill in missing values.""" + """Fill in missing values, given examples.""" ke: KnowledgeEngine # Choose model based on input, or use the default diff --git a/src/ontogpt/utils/parse_utils.py b/src/ontogpt/utils/parse_utils.py index cd043d7ae..2a897249c 100644 --- a/src/ontogpt/utils/parse_utils.py +++ b/src/ontogpt/utils/parse_utils.py @@ -1,4 +1,7 @@ """Utilities for parsing text.""" + +import re + from typing import List @@ -8,3 +11,35 @@ def split_on_one_of(text: str, separators: List[str]) -> List[str]: if sep in text: return text.split(sep) return [text] + +def get_section_of_interest(data, tag_of_interest): + # I blame adobe + # Find the index of the element that matches the case-insensitive regex pattern + start_index = None + pattern = re.compile(tag_of_interest, re.IGNORECASE) + if isinstance(data, str): + data = data.split("\n") + for i, item in enumerate(data): + if pattern.search(item): + start_index = i + break + + if start_index is not None: + # Find the index of the next element that starts with '<p>' + next_index = next( + ( + i + for i, item in enumerate(data[start_index + 1 :], start=start_index + 1) + if item.startswith("<p>") + ), + None, + ) + + if next_index is not None: + # Extract the desired element + result = data[next_index] + return result + else: + raise ValueError("No element starting with '<p>' found after the tag_of_interest") + else: + raise ValueError("No element matching the tag_of_interest found in the list.") \ No newline at end of file From 5422e33673a15ff2087ab76592f5c5f6f4acbc50 Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 13:09:43 -0400 Subject: [PATCH 17/40] Move get_kanjee_prompt to clinical_cases utils --- src/ontogpt/cli.py | 33 ----------------------------- src/ontogpt/utils/clinical_cases.py | 33 +++++++++++++++++++++++++++++ 2 files changed, 33 insertions(+), 33 deletions(-) create mode 100644 src/ontogpt/utils/clinical_cases.py diff --git a/src/ontogpt/cli.py b/src/ontogpt/cli.py index a269ba1c2..ed3096993 100644 --- a/src/ontogpt/cli.py +++ b/src/ontogpt/cli.py @@ -1315,39 +1315,6 @@ def run_multilingual_analysis( ) -def get_kanjee_prompt() -> str: - """Prompt from Kanjee et al. 2023.""" - prompt = ( - "I am running an experiment on a clinicopathological case conference to see " - "how your diagnoses compare with those of human experts. I am going to give " - "you part of a medical case. These have all been published in the New England " - "Journal of Medicine. You are not trying to treat any patients. As you read the " - "case, you will notice that there are expert discussants giving their thoughts. " - 'In this case, you are "Dr. GPT-4," an Al language model who is discussing ' - "the case along with human experts. A clinicopathological case conference has " - "several unspoken rules. The first is that there is most often a single definitive " - "diagnosis (though rarely there may be more than one), and it is a diagnosis that " - "is known today to exist in humans. The diagnosis is almost always confirmed by " - "some sort of clinical pathology test or anatomic pathology test, though in " - "rare cases when such a test does not exist for a diagnosis the diagnosis can " - "instead be made using validated clinical criteria or very rarely just confirmed " - "by expert opinion. You will be told at the end of the case description whether " - "a diagnostic test/tests are being ordered, which you can assume will make the " - "diagnosis/diagnoses. After you read the case, I want you to give two pieces of " - "information. The first piece of information is your most likely diagnosis/diagnoses. " - "You need to be as specific as possible -- the goal is to get the correct answer, " - "not a broad category of answers. You do not need to explain your reasoning, just " - "give the diagnosis/diagnoses. The second piece of information is to give a robust " - "differential diagnosis, ranked by their probability so that the most likely " - "diagnosis is at the top, and the least likely is at the bottom. There is no limit " - "to the number of diagnoses on your differential. You can give as many diagnoses " - "as you think are reasonable. You do not need to explain your reasoning, just list" - " the diagnoses. Again, the goal is to be as specific as possible with each of the " - "diagnoses. Do you have any questions, Dr. GPT-4?\n\nHere is the case:" - ) - return prompt - - @main.command() @inputfile_option @output_option_txt diff --git a/src/ontogpt/utils/clinical_cases.py b/src/ontogpt/utils/clinical_cases.py new file mode 100644 index 000000000..6c8cf704d --- /dev/null +++ b/src/ontogpt/utils/clinical_cases.py @@ -0,0 +1,33 @@ +"""Utilities for working with clinical case reports.""" + +def get_kanjee_prompt() -> str: + """Prompt from Kanjee et al. 2023.""" + prompt = ( + "I am running an experiment on a clinicopathological case conference to see " + "how your diagnoses compare with those of human experts. I am going to give " + "you part of a medical case. These have all been published in the New England " + "Journal of Medicine. You are not trying to treat any patients. As you read the " + "case, you will notice that there are expert discussants giving their thoughts. " + 'In this case, you are "Dr. GPT-4," an Al language model who is discussing ' + "the case along with human experts. A clinicopathological case conference has " + "several unspoken rules. The first is that there is most often a single definitive " + "diagnosis (though rarely there may be more than one), and it is a diagnosis that " + "is known today to exist in humans. The diagnosis is almost always confirmed by " + "some sort of clinical pathology test or anatomic pathology test, though in " + "rare cases when such a test does not exist for a diagnosis the diagnosis can " + "instead be made using validated clinical criteria or very rarely just confirmed " + "by expert opinion. You will be told at the end of the case description whether " + "a diagnostic test/tests are being ordered, which you can assume will make the " + "diagnosis/diagnoses. After you read the case, I want you to give two pieces of " + "information. The first piece of information is your most likely diagnosis/diagnoses. " + "You need to be as specific as possible -- the goal is to get the correct answer, " + "not a broad category of answers. You do not need to explain your reasoning, just " + "give the diagnosis/diagnoses. The second piece of information is to give a robust " + "differential diagnosis, ranked by their probability so that the most likely " + "diagnosis is at the top, and the least likely is at the bottom. There is no limit " + "to the number of diagnoses on your differential. You can give as many diagnoses " + "as you think are reasonable. You do not need to explain your reasoning, just list" + " the diagnoses. Again, the goal is to be as specific as possible with each of the " + "diagnoses. Do you have any questions, Dr. GPT-4?\n\nHere is the case:" + ) + return prompt \ No newline at end of file From c2d5c96c327601370485c7a7e7a371e04d288573 Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 13:14:18 -0400 Subject: [PATCH 18/40] Add examples for synonyms command --- src/ontogpt/cli.py | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/src/ontogpt/cli.py b/src/ontogpt/cli.py index ed3096993..44d11689a 100644 --- a/src/ontogpt/cli.py +++ b/src/ontogpt/cli.py @@ -984,7 +984,15 @@ def convert( def synonyms( model, term, context, output, temperature, api_base, api_version, model_provider, **kwargs ): - """Extract synonyms.""" + """Extract synonyms. + + Examples: + + ontogpt synonyms -m ollama/llama3 --context "political" "abdicate" + + ontogpt synonyms -m ollama/llama3 --context "biological" "dessicate" + + """ logging.info(f"Creating for {term}") if not model: From 36e436f9dbe897e6030d48742ecdcf6f48004ecc Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 13:18:35 -0400 Subject: [PATCH 19/40] Add example to search_and_extract command --- src/ontogpt/cli.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/src/ontogpt/cli.py b/src/ontogpt/cli.py index 44d11689a..37f6ac664 100644 --- a/src/ontogpt/cli.py +++ b/src/ontogpt/cli.py @@ -746,7 +746,12 @@ def search_and_extract( model_provider, **kwargs, ): - """Search for relevant literature and extract knowledge from it.""" + """Search for relevant literature through PubMed and extract knowledge from it. + + Example: + + ontogpt search-and-extract -m ollama/llama3 -t mondo_simple --keyword "kidney failure" + """ if not model: model = DEFAULT_MODEL @@ -991,7 +996,7 @@ def synonyms( ontogpt synonyms -m ollama/llama3 --context "political" "abdicate" ontogpt synonyms -m ollama/llama3 --context "biological" "dessicate" - + """ logging.info(f"Creating for {term}") From db94b8d7edbf98330df6429684060381217d4c88 Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 13:21:48 -0400 Subject: [PATCH 20/40] tweak example a bit --- src/ontogpt/cli.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontogpt/cli.py b/src/ontogpt/cli.py index 37f6ac664..386cedc35 100644 --- a/src/ontogpt/cli.py +++ b/src/ontogpt/cli.py @@ -750,7 +750,7 @@ def search_and_extract( Example: - ontogpt search-and-extract -m ollama/llama3 -t mondo_simple --keyword "kidney failure" + ontogpt search-and-extract -m ollama/llama3 -t phenotype --keyword "kidney failure" """ if not model: model = DEFAULT_MODEL From ce7a40beabb6a56a7c368afa1953cf9d5aeb815a Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 13:22:35 -0400 Subject: [PATCH 21/40] Don't truncate Wikipedia text --- src/ontogpt/cli.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/ontogpt/cli.py b/src/ontogpt/cli.py index 386cedc35..c36679454 100644 --- a/src/ontogpt/cli.py +++ b/src/ontogpt/cli.py @@ -705,10 +705,6 @@ def wikipedia_search( title = result["title"] text = client.text(title) logging.debug(f"Input text: {text}") - if len(text) > 4000: - # TODO - expand this to fit context limits better - # or add as cli option - text = text[:4000] results = ke.extract_from_text(text=text, show_prompt=show_prompt) write_extraction(results, output, output_format, ke, template) break From a545959d1ee21cd48c192242cb5be9be809bfdce Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 13:26:13 -0400 Subject: [PATCH 22/40] Add example for text generate and extract --- src/ontogpt/cli.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/ontogpt/cli.py b/src/ontogpt/cli.py index c36679454..4a3dbe8b5 100644 --- a/src/ontogpt/cli.py +++ b/src/ontogpt/cli.py @@ -399,7 +399,12 @@ def generate_extract( model_provider, **kwargs, ): - """Generate text and then extract knowledge from it.""" + """Generate text and then extract knowledge from it. + + Example: + + ontogpt generate-extract -m ollama/llama3 -t kidney "kidney failure" + """ if not model: model = DEFAULT_MODEL From 844fc061402a53fdb5914d16aeb4095420a6ac57 Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 13:33:20 -0400 Subject: [PATCH 23/40] Bump version to 1.0.0rc1 --- poetry.lock | 28 ++++++++++++++-------------- pyproject.toml | 6 +++--- 2 files changed, 17 insertions(+), 17 deletions(-) diff --git a/poetry.lock b/poetry.lock index e0de44808..482506637 100644 --- a/poetry.lock +++ b/poetry.lock @@ -529,17 +529,17 @@ files = [ [[package]] name = "boto3" -version = "1.34.144" +version = "1.34.145" description = "The AWS SDK for Python" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-1.34.144-py3-none-any.whl", hash = "sha256:b8433d481d50b68a0162c0379c0dd4aabfc3d1ad901800beb5b87815997511c1"}, - {file = "boto3-1.34.144.tar.gz", hash = "sha256:2f3e88b10b8fcc5f6100a9d74cd28230edc9d4fa226d99dd40a3ab38ac213673"}, + {file = "boto3-1.34.145-py3-none-any.whl", hash = "sha256:69d5afb7a017d07dd6bdfb680d2912d5d369b3fafa0a45161207d9f393b14d7e"}, + {file = "boto3-1.34.145.tar.gz", hash = "sha256:ac770fb53dde1743aec56bd8e56b7ee2e2f5ad42a37825968ec4ff8428822640"}, ] [package.dependencies] -botocore = ">=1.34.144,<1.35.0" +botocore = ">=1.34.145,<1.35.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.10.0,<0.11.0" @@ -548,13 +548,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.34.144" +version = "1.34.145" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">=3.8" files = [ - {file = "botocore-1.34.144-py3-none-any.whl", hash = "sha256:a2cf26e1bf10d5917a2285e50257bc44e94a1d16574f282f3274f7a5d8d1f08b"}, - {file = "botocore-1.34.144.tar.gz", hash = "sha256:4215db28d25309d59c99507f1f77df9089e5bebbad35f6e19c7c44ec5383a3e8"}, + {file = "botocore-1.34.145-py3-none-any.whl", hash = "sha256:2e72e262de02adcb0264ac2bac159a28f55dbba8d9e52aa0308773a42950dff5"}, + {file = "botocore-1.34.145.tar.gz", hash = "sha256:edf0fb4c02186ae29b76263ac5fda18b0a085d334a310551c9984407cf1079e6"}, ] [package.dependencies] @@ -4209,13 +4209,13 @@ tests = ["coverage", "pytest", "unittest-templates"] [[package]] name = "openai" -version = "1.35.15" +version = "1.36.0" description = "The official Python library for the openai API" optional = false python-versions = ">=3.7.1" files = [ - {file = "openai-1.35.15-py3-none-any.whl", hash = "sha256:1b9a6ada4239b91f38f51c426c6ee2746a2069c92cbf25ed8694e5ec00ff4597"}, - {file = "openai-1.35.15.tar.gz", hash = "sha256:307007e2036d57115612c1ecb50e9bc98fcc93537109a9f9efa1b4eedb2ea968"}, + {file = "openai-1.36.0-py3-none-any.whl", hash = "sha256:82b74ded1fe2ea94abb19a007178bc143675f1b6903cebd63e2968d654bb0a6f"}, + {file = "openai-1.36.0.tar.gz", hash = "sha256:a124baf0e1657d6156e12248642f88489cd030be8655b69bc1c13eb50e71a93d"}, ] [package.dependencies] @@ -4629,13 +4629,13 @@ requests = ">=2.28.1,<3.0.0" [[package]] name = "prefixmaps" -version = "0.2.4" +version = "0.2.5" description = "A python library for retrieving semantic prefix maps" optional = false python-versions = "<4.0,>=3.8" files = [ - {file = "prefixmaps-0.2.4-py3-none-any.whl", hash = "sha256:89bf0e6fb08c276f754f9624c42adf2e87c64ee92a3dde1f7eff01f22d85b512"}, - {file = "prefixmaps-0.2.4.tar.gz", hash = "sha256:ae86a1b31189d0516d199756d5808f75f44b39e86546c356cc78c0fe8d2078af"}, + {file = "prefixmaps-0.2.5-py3-none-any.whl", hash = "sha256:68caa04b3a6a8e058aa1c55affe32c62e44b564d031d63f768e267b796a1f3ee"}, + {file = "prefixmaps-0.2.5.tar.gz", hash = "sha256:aaccd2425ade2ea97a502c58be49fe8f3536e3d5e919712ae0358a39fc800799"}, ] [package.dependencies] @@ -7954,4 +7954,4 @@ web = ["Jinja2", "fastapi", "uvicorn"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.9.7 || >3.9.7,<4.0" -content-hash = "816c2636ad221e6922175af52f20658e6a45ea2e5d3f3934483e6d1df9b9985b" +content-hash = "3b217c3e12d0d391144575b14661017bfbb2cb7fa745951ac031307d783adbe6" diff --git a/pyproject.toml b/pyproject.toml index 1d997e513..824ab3792 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "ontogpt" -version = "0.3.15" +version = "1.0.0rc1" description = "OntoGPT" authors = ["Chris Mungall <cjmungall@lbl.gov>", "J. Harry Caufield <jhc@lbl.gov>"] license = "BSD-3" @@ -12,14 +12,14 @@ python = ">=3.9,<3.9.7 || >3.9.7,<4.0" Jinja2 = {version = ">=3.1.2", optional = true} aiohttp = ">=3.8.4" beautifulsoup4 = ">=4.11.1" -bioc = ">=2.0.post5" +bioc = ">=2.0" cachier = ">=2.1.0" click = ">=8.1.3" fastapi = {version = ">=0.88.0", optional = true} gilda = ">=1.0.0" inflect = ">=6.0.2" inflection = ">=0.5.1" -linkml = "^1.5.7" +linkml = "^1.8.0" linkml-owl = "^0.3.0" myst-parser = {version = ">=0.18.1", extras = ["docs"], optional = true} oaklib = ">=0.5.28" From 2eacee8d4ca9e99c6c26a85cb3056d9c7148e2e0 Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 13:34:23 -0400 Subject: [PATCH 24/40] Bump linkml to ^1.8.0 --- poetry.lock | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/poetry.lock b/poetry.lock index 482506637..dba0d5c14 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2612,20 +2612,20 @@ files = [ [package.dependencies] attrs = ">=22.2.0" -fqdn = {version = "*", optional = true, markers = "extra == \"format-nongpl\""} -idna = {version = "*", optional = true, markers = "extra == \"format-nongpl\""} -isoduration = {version = "*", optional = true, markers = "extra == \"format-nongpl\""} -jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format-nongpl\""} +fqdn = {version = "*", optional = true, markers = "extra == \"format\""} +idna = {version = "*", optional = true, markers = "extra == \"format\""} +isoduration = {version = "*", optional = true, markers = "extra == \"format\""} +jsonpointer = {version = ">1.13", optional = true, markers = "extra == \"format\""} jsonschema-specifications = ">=2023.03.6" referencing = ">=0.28.4" -rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format-nongpl\""} +rfc3339-validator = {version = "*", optional = true, markers = "extra == \"format\""} rfc3986-validator = {version = ">0.1.0", optional = true, markers = "extra == \"format-nongpl\""} rfc3987 = {version = "*", optional = true, markers = "extra == \"format\""} rpds-py = ">=0.7.1" -uri-template = {version = "*", optional = true, markers = "extra == \"format-nongpl\""} +uri-template = {version = "*", optional = true, markers = "extra == \"format\""} webcolors = [ - {version = ">=1.11", optional = true, markers = "extra == \"format\""}, {version = ">=24.6.0", optional = true, markers = "extra == \"format-nongpl\""}, + {version = ">=1.11", optional = true, markers = "extra == \"format\""}, ] [package.extras] @@ -7954,4 +7954,4 @@ web = ["Jinja2", "fastapi", "uvicorn"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.9.7 || >3.9.7,<4.0" -content-hash = "3b217c3e12d0d391144575b14661017bfbb2cb7fa745951ac031307d783adbe6" +content-hash = "d30ca6958ab776c6bcf29ce62d2c4098453a222c5a9a450ae4600c3a961a858e" From 41a400a735f290fc5fccb4fb95127dfb0903bebd Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 13:35:46 -0400 Subject: [PATCH 25/40] Remove streamlit - not using here yet --- poetry.lock | 212 +------------------------------------------------ pyproject.toml | 1 - 2 files changed, 4 insertions(+), 209 deletions(-) diff --git a/poetry.lock b/poetry.lock index dba0d5c14..f2a4775d5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -167,31 +167,6 @@ files = [ {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, ] -[[package]] -name = "altair" -version = "5.3.0" -description = "Vega-Altair: A declarative statistical visualization library for Python." -optional = false -python-versions = ">=3.8" -files = [ - 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poetry run papermill $< $@ -p experiment_results analysis/$*-enrichment-summary-2.yaml From e24646325c80f5f030be48d9fa4b1738dcdea975 Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 13:41:28 -0400 Subject: [PATCH 27/40] Move older notebooks to old --- .../Enrichment-Results-Analysis.ipynb | 0 notebooks/{ => old}/parse_msigdb.ipynb | 0 notebooks/output1.yaml | 106 ++++++++ notebooks/output2.yaml | 175 +++++++++++++ notebooks/output3.yaml | 235 ++++++++++++++++++ notebooks/text.txt | 1 + notebooks/text2.txt | 1 + 7 files changed, 518 insertions(+) rename notebooks/{ => old}/Enrichment-Results-Analysis.ipynb (100%) rename notebooks/{ => old}/parse_msigdb.ipynb (100%) create mode 100644 notebooks/output1.yaml create mode 100644 notebooks/output2.yaml create mode 100644 notebooks/output3.yaml create mode 100644 notebooks/text.txt create mode 100644 notebooks/text2.txt diff --git a/notebooks/Enrichment-Results-Analysis.ipynb b/notebooks/old/Enrichment-Results-Analysis.ipynb similarity index 100% rename from notebooks/Enrichment-Results-Analysis.ipynb rename to notebooks/old/Enrichment-Results-Analysis.ipynb diff --git a/notebooks/parse_msigdb.ipynb b/notebooks/old/parse_msigdb.ipynb similarity index 100% rename from notebooks/parse_msigdb.ipynb rename to notebooks/old/parse_msigdb.ipynb diff --git a/notebooks/output1.yaml b/notebooks/output1.yaml new file mode 100644 index 000000000..5496a7de6 --- /dev/null +++ b/notebooks/output1.yaml @@ -0,0 +1,106 @@ +--- +input_text: Spain is a significant contributor to the global agricultural sector, + with its primary exports demonstrating the country's diverse climate and agricultural + capacity. The nation leads the world in olive oil production and export, renowned + for its quality. Spain is also one of the top wine producers globally, with notable + regions including Rioja and Ribera del Duero. It exports a wide range of fruits, + particularly citrus fruits such as oranges and lemons from Valencia, as well as + peaches, strawberries, melons, and apples. Vegetable exports are substantial, with + tomatoes, peppers, cucumbers, and lettuce being predominant, especially from the + Almería region known for its greenhouse production. Spain is recognized for its + premium pork products, notably jamón ibérico and jamón serrano, and is a leading + exporter of nuts, particularly almonds and hazelnuts. Additionally, Spain exports + significant quantities of fish and seafood, including sardines, tuna, and shrimp, + facilitated by its extensive coastline and fishing traditions. +raw_completion_output: |- + terms: Olive oil;Wine;Citrus fruits;Oranges;Lemons;Peaches;Strawberries;Melons;Apples;Tomatoes;Peppers;Cucumbers;Lettuce;Pork products;Jamón ibérico;Jamón serrano;Nuts;Almonds;Hazelnuts;Fish;Seafood;Sardines;Tuna;Shrimp + label: Spain +prompt: |+ + From the text below, extract the following entities in the following format: + + terms: <A semicolon-separated list of any Food Ontology terms.> + label: <The label (name) of the named thing> + + + Text: + Spain is a significant contributor to the global agricultural sector, with its primary exports demonstrating the country's diverse climate and agricultural capacity. The nation leads the world in olive oil production and export, renowned for its quality. Spain is also one of the top wine producers globally, with notable regions including Rioja and Ribera del Duero. It exports a wide range of fruits, particularly citrus fruits such as oranges and lemons from Valencia, as well as peaches, strawberries, melons, and apples. Vegetable exports are substantial, with tomatoes, peppers, cucumbers, and lettuce being predominant, especially from the Almería region known for its greenhouse production. Spain is recognized for its premium pork products, notably jamón ibérico and jamón serrano, and is a leading exporter of nuts, particularly almonds and hazelnuts. Additionally, Spain exports significant quantities of fish and seafood, including sardines, tuna, and shrimp, facilitated by its extensive coastline and fishing traditions. + + === + +extracted_object: + id: c2a2b5c7-c262-46b7-a3d7-a733a5a83c7a + label: Spain + terms: + - FOODON:03301826 + - AUTO:Wine + - FOODON:00003324 + - FOODON:03315106 + - FOODON:03315104 + - FOODON:03315502 + - FOODON:00003443 + - FOODON:00003597 + - FOODON:00002473 + - FOODON:03301453 + - FOODON:00003520 + - FOODON:00003415 + - FOODON:00001998 + - AUTO:Pork%20products + - AUTO:Jam%C3%B3n%20ib%C3%A9rico + - AUTO:Jam%C3%B3n%20serrano + - FOODON:03303171 + - FOODON:00003523 + - FOODON:00002933 + - FOODON:03411222 + - AUTO:Seafood + - FOODON:03411558 + - FOODON:03411269 + - FOODON:03411237 +named_entities: + - id: FOODON:03301826 + label: Olive oil + - id: AUTO:Wine + label: Wine + - id: FOODON:00003324 + label: Citrus fruits + - id: FOODON:03315106 + label: Oranges + - id: FOODON:03315104 + label: Lemons + - id: FOODON:03315502 + label: Peaches + - id: FOODON:00003443 + label: Strawberries + - id: FOODON:00003597 + label: Melons + - id: FOODON:00002473 + label: Apples + - id: FOODON:03301453 + label: Tomatoes + - id: FOODON:00003520 + label: Peppers + - id: FOODON:00003415 + label: Cucumbers + - id: FOODON:00001998 + label: Lettuce + - id: AUTO:Pork%20products + label: Pork products + - id: AUTO:Jam%C3%B3n%20ib%C3%A9rico + label: Jamón ibérico + - id: AUTO:Jam%C3%B3n%20serrano + label: Jamón serrano + - id: FOODON:03303171 + label: Nuts + - id: FOODON:00003523 + label: Almonds + - id: FOODON:00002933 + label: Hazelnuts + - id: FOODON:03411222 + label: Fish + - id: AUTO:Seafood + label: Seafood + - id: FOODON:03411558 + label: Sardines + - id: FOODON:03411269 + label: Tuna + - id: FOODON:03411237 + label: Shrimp diff --git a/notebooks/output2.yaml b/notebooks/output2.yaml new file mode 100644 index 000000000..1f562c55d --- /dev/null +++ b/notebooks/output2.yaml @@ -0,0 +1,175 @@ +--- +input_text: Zambia and the DR Congo are situated in the central African Copperbelt, + which is part of the Lufilian geological structure arc stretching over from Kolwezi + in Katanga Province in the DRC to Luanshya in Copperbelt Province in Zambia. The + area has large copper-cobalt deposits of which the extraction causes severe ecosystem + damage due to pollution of water, food crops, and the ambient air negatively impacting + population health. Contamination of drinking water for domestic use and foods (cereals, + roots and tubers, vegetables, and fruits) was determined by assessing the contents + of trace metals including Mn, Ni, Pb, Zn, Co, As, U, Cd, and Cu and through a questionnaire + for environmental damage. Food samples were analyzed by inductively coupled argon + plasma/optical emission spectroscopy (ICP-OES), while water and urine samples were + analyzed by inductively coupled argon plasma mass spectrometry (ICP-MS). Concentrations + of Ni, Pb, and Cd were higher in almost all food crops, although Cu was more in + samples of Cucurbita maxima and Amaranthus hybridus. Mean contents (μg/L) of Mn, + Zn, Cd, Pb, and U were, respectively, 5,454.6, 2552.2, 138.7, 39.7, 2361.1, and + 21.4 in the DRC and 108.9, 543.3, 0.3, 0.2, 1.5, and 0.5 in Zambia, being significantly + higher and always far above World Health Organization maximum limits in the DRC. + Urine samples taken only from the DRC contained trace metals with children's samples + being more contaminated than adult ones. Our results conclusively echo the most + critical challenges of toxic pollutants causing numerous health issues among the + population. Given an outcry among households adjacent to mines about land degradation + and food spoilage, and health problems over years, joint efforts are needed from + public and private sectors for stringent mining exploitation monitoring for sustainable + governance to protect the environment and ensure food and nutrition safety, and + population well-being in Zambia and the DR Congo. +raw_completion_output: |- + location: Kolwezi;Katanga Province;Luanshya;Copperbelt Province + environmental_material: water;food crops;ambient air;drinking water;cereals;roots and tubers;vegetables;fruits;food samples;urine samples + environments: Copperbelt;Lufilian geological structure arc + causal_relationships: effect of extraction on ecosystem damage;effect of pollution on population health;effect of trace metals on contamination of drinking water and foods;effect of pollutants on health issues + variables: Mn;Ni;Pb;Zn;Co;As;U;Cd;Cu;toxic pollutants;health issues;land degradation;food spoilage;children's samples;adult samples + measurements: Mn-5454.6 μg/L;Zn-2552.2 μg/L;Cd-138.7 μg/L;Pb-39.7 μg/L;U-2361.1 μg/L;Mn-108.9 μg/L;Zn-543.3 μg/L;Cd-0.3 μg/L;Pb-0.2 μg/L;U-1.5 μg/L;U-0.5 μg/L +prompt: |+ + Split the following piece of text into fields in the following format: + + value: <the value of the measurement> + unit: <the unit of the measurement> + + + Text: + U-0.5 μg/L + + === + +extracted_object: + location: + - AUTO:Kolwezi + - AUTO:Katanga%20Province + - AUTO:Luanshya + - GAZ:00009425 + environmental_material: + - ENVO:00002006 + - ENVTHES:20523 + - ENVTHES:23 + - ENVO:00003064 + - AUTO:cereals + - AUTO:roots%20and%20tubers + - AUTO:vegetables + - ENVTHES:20576 + - ENVTHES:20523 + - ENVTHES:10152 + environments: + - AUTO:Copperbelt + - ENVTHES:10358 + causal_relationships: + - cause: AUTO:extraction + effect: ENVO:01001110 + - cause: ENVO:02500036 + effect: ENVTHES:20715 + - cause: ENVO:01001069 + effect: ENVO:00003064 + - cause: ENVTHES:20893 + effect: AUTO:health%20issues + variables: + - AUTO:Mn + - AUTO:Ni + - AUTO:Pb + - AUTO:Zn + - AUTO:Co + - AUTO:As + - AUTO:U + - AUTO:Cd + - AUTO:Cu + - ENVTHES:20893 + - AUTO:health%20issues + - ENVO:02500005 + - ENVTHES:20523 + - ENVTHES:10152 + - ENVTHES:10152 + measurements: + - value: '5454.6' + unit: AUTO:%CE%BCg/L + - value: '2552.2' + unit: AUTO:%CE%BCg/L + - value: '39.7' + unit: AUTO:%CE%BCg/L + - value: '2361.1' + unit: AUTO:%CE%BCg/L + - value: '108.9' + unit: AUTO:%CE%BCg/L + - value: '0.3' + unit: AUTO:%CE%BCg/L + - value: '0.2' + unit: AUTO:%CE%BCg/L + - value: '1.5' + unit: AUTO:%CE%BCg/L + - value: '0.5' + unit: AUTO:%CE%BCg/L +named_entities: + - id: AUTO:Kolwezi + label: Kolwezi + - id: AUTO:Katanga%20Province + label: Katanga Province + - id: AUTO:Luanshya + label: Luanshya + - id: GAZ:00009425 + label: Copperbelt Province + - id: ENVO:00002006 + label: water + - id: ENVTHES:20523 + label: food crops + - id: ENVTHES:23 + label: ambient air + - id: ENVO:00003064 + label: drinking water + - id: AUTO:cereals + label: cereals + - id: AUTO:roots%20and%20tubers + label: roots and tubers + - id: AUTO:vegetables + label: vegetables + - id: ENVTHES:20576 + label: fruits + - id: ENVTHES:10152 + label: urine samples + - id: AUTO:Copperbelt + label: Copperbelt + - id: ENVTHES:10358 + label: Lufilian geological structure arc + - id: AUTO:extraction + label: extraction + - id: ENVO:01001110 + label: ecosystem damage + - id: ENVO:02500036 + label: pollution + - id: ENVTHES:20715 + label: population health + - id: ENVO:01001069 + label: trace metals + - id: ENVTHES:20893 + label: pollutants + - id: AUTO:health%20issues + label: health issues + - id: AUTO:Mn + label: Mn + - id: AUTO:Ni + label: Ni + - id: AUTO:Pb + label: Pb + - id: AUTO:Zn + label: Zn + - id: AUTO:Co + label: Co + - id: AUTO:As + label: As + - id: AUTO:U + label: U + - id: AUTO:Cd + label: Cd + - id: AUTO:Cu + label: Cu + - id: ENVO:02500005 + label: land degradation + - id: AUTO:%CE%BCg/L + label: μg/L diff --git a/notebooks/output3.yaml b/notebooks/output3.yaml new file mode 100644 index 000000000..d68555228 --- /dev/null +++ b/notebooks/output3.yaml @@ -0,0 +1,235 @@ +--- +input_text: |- + Title: Impacts of Trace Metals Pollution of Water, Food Crops, and Ambient Air on Population Health in Zambia and the DR Congo. + Keywords: + PMID: 35844936 + PMCID: PMC9277192 + Zambia and the DR Congo are situated in the central African Copperbelt, which is part of the Lufilian geological structure arc stretching over from Kolwezi in Katanga Province in the DRC to Luanshya in Copperbelt Province in Zambia. The area has large copper-cobalt deposits of which the extraction causes severe ecosystem damage due to pollution of water, food crops, and the ambient air negatively impacting population health. Contamination of drinking water for domestic use and foods (cereals, roots and tubers, vegetables, and fruits) was determined by assessing the contents of trace metals including Mn, Ni, Pb, Zn, Co, As, U, Cd, and Cu and through a questionnaire for environmental damage. Food samples were analyzed by inductively coupled argon plasma/optical emission spectroscopy (ICP-OES), while water and urine samples were analyzed by inductively coupled argon plasma mass spectrometry (ICP-MS). Concentrations of Ni, Pb, and Cd were higher in almost all food crops, although Cu was more in samples of Cucurbita maxima and Amaranthus hybridus. Mean contents (μg/L) of Mn, Zn, Cd, Pb, and U were, respectively, 5,454.6, 2552.2, 138.7, 39.7, 2361.1, and 21.4 in the DRC and 108.9, 543.3, 0.3, 0.2, 1.5, and 0.5 in Zambia, being significantly higher and always far above World Health Organization maximum limits in the DRC. Urine samples taken only from the DRC contained trace metals with children's samples being more contaminated than adult ones. Our results conclusively echo the most critical challenges of toxic pollutants causing numerous health issues among the population. Given an outcry among households adjacent to mines about land degradation and food spoilage, and health problems over years, joint efforts are needed from public and private sectors for stringent mining exploitation monitoring for sustainable governance to protect the environment and ensure food and nutrition safety, and population well-being in Zambia and the DR Congo.Copyright © 2022 A. Muimba-Kankolongo et al. 1. Introduction Zambia and the DR Congo (DRC) are situated in the central African Copperbelt region, which is part of the Lufilian geological structure arc that stretches over more than 500 km from Kolwezi in the former Katanga Province in the DRC to Luanshya in Copperbelt Province in Zambia [1]. The arc contains large reserves of copper and cobalt minerals [2], which represent the mainstay of the two countries' economy [3–8]. With about 28% contribution to the GNP and 70% export value [6], mining exploitation remains the main source of DRC's foreign currencies [6, 7]. Similarly, the mining sector is Zambia's most sensitive economic sector owing to its linkage to the export market, and copper contributes about 70% of foreign earnings [9]. The mining industry only contributes about 9.90% to GDP, 77% to export earnings, and 27.77% to country employment [10]. Besides public and private industrial mining, artisanal mine productions are also widespread [11–15] and often work in the form of cooperatives of artisan miners—also known as formal artisanal mining—leading to the establishment of a middle class of Congolese and Zambians contributing to the integrated development of grassroot communities. They operate on industrial mining concessions using nonstandard extraction practices such as sieving the soil in rivers, thereby causing severe environmental pollution. There are currently numerous public, parastatal, and private companies and informal artisanal mining operating in the mining sector in Zambia and in the DRC [7, 14, 15]. Brummett et al. [16] recorded the reduction in water quality through mining pollution as a major threat to freshwater ecosystems, and Banks et al. [17] and Pulles et al. [18] noted that discharges of contaminants in water resources constitute the main environmental challenges to most mining exploitations. Much of the sub-Saharan Africa including the central Africa Copperbelt comprises more poor rural communities that depend on agriculture for livelihoods and as an important source of commodities' exports and intraregional trade [19]. The agricultural sector in the region is dominated by crop production mainly by smallholder farmers—because of the climate change that has exacerbated weather variability—over-depending on rainfed agricultural production of roots and tubers, plantains, maize, rice, groundnuts, beans, sorghum, millets, and vegetables [19–22]. Estimates from the World Bank [23] indicate that the value addition to GDP attributable to agriculture in the DRC and Zambia is 42.9% and 21.6%, respectively. About 75% of the population is engaged in agriculture, largely subsistence farming that contributes about 60% to the overall production output [24]. Nevertheless, the performance of agriculture in the central Africa Copperbelt region in terms of food production and security has been lacking far behind mainly due to recurrent prolonged droughts, making food insecurity a major challenge [25, 26]. Moreover, food security is compromised by the degradation of farmlands and the environment resulting from mineral extractions [27], often culminating in food shortages and famine. The community's inhabitants are perpetually prone to hunger, malnutrition, and poverty. Contaminants from mines and metallurgic industries pollute water, soil, and the ambient air affecting the growth pattern and well-being, especially for children. For decades, mining activities including construction, exploitation, and maintenance have caused severe damage to the regional ecosystem resulting in land-use change and associated negative impacts on environments such as deforestation, erosion, alteration of agricultural soil properties, contamination of local streams and wetlands, and an increase in noise level, dust, and smoke plume emissions [27, 28]. Pollution of the ambient air from industrial activities caused mainly by pollutants being transported over long distances after their release into the environment has also been the source of health concerns. Other negative impact communities living on fringe of the mines endure include the impacts on rainfall pattern modification becoming less and often starting late in the year leading to the decline of the forest cover and considerably decreasing forest resources used for their well-being [27, 29, 30]. Health threats posed to residents from prolonged exposure to toxic trace metals and metalloid can only be determined by their daily dietary intake through ingestion and inhalation pathways. Individuals' life span trend and their well-being could also serve as broad indicators for their physiological food uptake, digestion, and storage as well [31, 32]. Numerous studies have been carried out in the DRC in relation to human body accumulation of pollutants and showed high amounts of pollutants in the blood and urine of inhabitants in the mining areas including mineworkers, residents of an urban neighbourhood that had been transformed into an artisanal cobalt mine, and children with strong evidence of exposure-related oxidative DNA damage [15, 33, 34]. In contrast in Zambia, only investigations in children suffering from lead poisoning are well established in the plomb mining area in Kabwe town that has left a legacy of significant environmental pollution [28, 35]. Aside from the threat of increased and prolonged exposure to trace metal contaminants in food crops that were sampled in this study, we also acknowledged that local communities in the two countries have a varied and diversified food staples depending on ethnicity, culture, and where they live. Hence, our study could have also included foods such as fresh, frozen, and smoked fish, fresh and smoked meat (goat, chicken, beef, pork), eggs, eggplants, rape, okra, poultry, caterpillars, grasshoppers and flying termites, and lentils that are commonly utilized in the diet to fully evaluate the body burden of trace metals among the devastated populations. Although ambient air pollution has been thoroughly investigated by others [15, 36–40], data on the identification and distribution of metal particle size are critically needed both from emission sources and in the ambient air. Particle size data on trace metals can be used to appraise the efficiency of emission control devices, evaluate the inhalation hazard, determine the timing of metals in the atmosphere, and assess visibility reduction and for a wide range of other applications including understanding atmospheric transformations. Given the enormous scale of damage to the ecosystems resulting from mineral extraction and operations of metallurgic industries that generate hazardous wastes containing dissolved toxic metals over the years, there has been an outcry among households adjacent to mines about land degradation, water and air pollution, and food spoilage. This study was carried out to investigate the perceptions of inhabitants living around mining areas and other stakeholders as regards the environmental and social impacts on the communities from industrial activities with the objectives to improve the population health and livelihood. 2. Materials and Methods 2.1. Study Sites This study was concentrated in the copper-cobalt producing areas of Zambia and the DRC (Figure 1) from September 2010 to September 2012 to enable a cross-country assessment of landscape pollution and impacts on population health. They were Haut-Katanga Province (Lat. 11°39′52.84″S, Long. 27°28′46.38 E, Alt. 1239 m) in the southeastern DRC where Gécamines—the state mining company—with its subsidiary industries have huge concessions covering approximately 30,000 km2 around the towns of Likasi (Central Group), Kipushi (Southwest Group), and Lubumbashi (East Group), and the Copperbelt Province in Zambia (Lat. 13°03′25.23″S, Long. 27°32′58.50″E, Alt. +raw_completion_output: |- + location: Haut-Katanga Province; Likasi; Kipushi; Lubumbashi + environmental_material: water; food crops; ambient air; soils; local streams; wetlands + environments: mining areas; urban neighbourhood; farmland + causal_relationships: impacts of trace metals pollution on population health; effect of contamination of drinking water on health; effect of pollutants on food crops; impact of land degradation on food security; impacts of heavy metals on well-being + variables: trace metals (Mn, Ni, Pb, Zn, Co, As, U, Cd, Cu) content; food contamination; water quality; air quality; health outcomes; land degradation; food insecurity + measurements: Mean contents (μg/L) of Mn, Zn, Cd, Pb, and U in the DRC: 5,454.6, 2552.2, 138.7, 39.7, 2361.1, 21.4; Mean contents (μg/L) of Mn, Zn, Cd, Pb, and U in Zambia: 108.9, 543.3, 0.3, 0.2, 1.5, 0.5 +prompt: |+ + From the text below, extract the following entities in the following format: + + value: <the value of the measurement> + unit: <the unit of the measurement> + + + Text: + Mean contents (μg/L) of Mn, Zn, Cd, Pb, and U in Zambia: 108.9, 543.3, 0.3, 0.2, 1.5, 0.5 + + === + +extracted_object: + location: + - GAZ:00235446 + - Likasi + - Kipushi + - Lubumbashi + environmental_material: + - ENVO:00002006 + - ENVTHES:20523 + - ENVTHES:23 + - ENVO:00001998 + - ENVTHES:21796 + - ENVO:00000035 + environments: + - ENVTHES:21533 + - urban neighbourhood + - farmland + causal_relationships: + - cause: ENVO:02500036 + effect: ENVTHES:20715 + - cause: ENVO:00003064 + effect: health + - cause: ENVTHES:20893 + effect: ENVTHES:20523 + - cause: ENVO:02500005 + effect: ENVTHES:21483 + - cause: PATO:0000582 + effect: well-being + variables: + - PATO:0000025 + - ENVTHES:20523 + - ENVTHES:22312 + - ENVO:00002005 + - health outcomes + - ENVO:02500005 + - ENVTHES:20523 + measurements: + - value: '21.4' + unit: μg/L + - value: '0.5' + unit: μg/L +named_entities: + - id: GAZ:00235446 + label: Haut-Katanga Province + - id: ENVO:00002006 + label: water + - id: ENVTHES:20523 + label: food crops + - id: ENVTHES:23 + label: ambient air + - id: ENVO:00001998 + label: soils + - id: ENVTHES:21796 + label: local streams + - id: ENVO:00000035 + label: wetlands + - id: ENVTHES:21533 + label: mining areas + - id: ENVO:02500036 + label: trace metals pollution + - id: ENVTHES:20715 + label: population health + - id: ENVO:00003064 + label: contamination of drinking water + - id: ENVTHES:20893 + label: pollutants + - id: ENVO:02500005 + label: land degradation + - id: ENVTHES:21483 + label: food security + - id: PATO:0000582 + label: heavy metals + - id: PATO:0000025 + label: trace metals (Mn, Ni, Pb, Zn, Co, As, U, Cd, Cu) content + - id: ENVTHES:22312 + label: water quality + - id: ENVO:00002005 + label: air quality +--- +input_text: |- + Title: Impacts of Trace Metals Pollution of Water, Food Crops, and Ambient Air on Population Health in Zambia and the DR Congo. + Keywords: + PMID: 35844936 + PMCID: PMC9277192 + 1247 m) where various companies including Konkola Copper Mines (KCM), Nchanga Mines, Mopani Copper Mines, Chambishi Metals, Roan Antelope Mining Corporation, and Luanshya and Kansanshi Mines extract minerals. KCM, one of the largest mining companies belonging to Vedanta, operates underground mines and open-pit mines and metallurgical plants with operations located on one of the highest-grade copper seams at Nchanga, Konkola, and Nkana in Kitwe and Nampundwe. A total of three sampling locations were specifically selected within each country based on recent proliferation of mines and previous reports on environmental contamination from plant effluents, spills, and tailings dam discharges and to have a wide distribution of sampling sites across the two countries. They were cities of Lubumbashi and Likasi, and Kipushi Territory in Haut-Katanga Province in the DRC, and Chingola, Kitwe, and Luanshya Districts in Zambia. Within each location, several sites were identified for sampling either in the proximity of intense mining and metallurgic activities or far away as controls based on the premises of past farmland degradation, potential degrees of high or low exposure, easy accessibility, and avoiding health risk due to possible irradiation from dangerous mining areas. They included Kabecha, Tshansansa, and Kasongo sites in Lubumbashi; SNCC-Shituru, Gécamines-Shituru, and Panda cities, and Kansalabwe village in Likasi; and Mungoshi and Douane areas, Betty City, Kampemba farm, and Nkumanwa village in Kipushi for the DRC. In Zambia, they were Shimulala, Heleni-Kasenji, Kalipenta, Pule, and Chama villages in Chingola; Roan area, and Mpatamatu and Mwansa villages in Luanshya; and Chankalamu village and Wusakile and Nkana West compounds in Kitwe. 2.2. Approaches to Sample Collection and Analysis 2.2.1. Collection and Analysis of Food Crop Samples Prioritised samples that were at the full stage of development were collected with permission in residents' gardens following the sites mapping around mine areas and far away and local harvesting practices, considering grains, leaves, stems, tubers/roots, and bulbs as plant parts for laboratory analysis. Precautions were taken to have both women and men during the briefing, which focused on hazardous chemicals for which long-term exposure might have potential effects on their health. After harvest, samples were immediately kept in paper bags, labeled accordingly, and kept in a refrigerator. In total, the samples included root and tuber crops (n = 48), leafy vegetables (n = 143), fruits (n = 51), bulbs (n = 5), and other plants (n = 33) that are also locally consumed. Out of these, 205 were from areas of intense mining and metallurgic industry activities, whereas 75 were derived from areas distant from these activities. Collected samples were pretreated individually by rinsing twice in running tap water and 3-4 times with sterile distilled water to remove any soil particles and other plant debris from fields and blotted dry before slicing into small pieces using a sterile knife. They were then oven-dried at 70°C to constant weight for 48 hours and separately homogenized by mechanical grinding using sterile porcelain mortars and pestles made from China. The weight of each sample powder was recorded before wrapping it in minigrip bags, which were maintained at room ambient temperature for further use. Thereafter, study samples were air-dispatched to soil and occupational and medicinal laboratories in Belgium for analysis. As described by Muimba-Kankolongo et al. [31], ground oven-dried powder samples of various food crops were crushed and sequentially digested in HNO3 (3 successive runs of dissolution in HNO3 (1 mL Suprapur 70%) followed by evaporation to dryness for 4 h at 110°C) and by microwave heating (250 W × 5 min; 400 W × 5 min; 650 W × 10 min; 250 W × 5 min) and then left to cool, and contents were filtered through Whatman filter paper no. 42 and kept in a final solution of 2% HCl and analyzed for total metal content by inductively coupled plasma/optical emission spectroscopy (ICP-OES, Perkin-Elmer Optima 3300 DV, Norwalk, CT, USA) in the Louvain Centre for Toxicology and Applied Pharmacology (Université catholique de Louvain, Belgium). At concentrations of b5 μg·Co/L in the digest, measurements were made by ICP-MS (Thermo X Series I) in He mode using Ga internal standard. Certified reference material NIST SRM-1573a (tomato leaves, National Institute of Standards and Technology, Gaithersburg, Germany, certified value = 0.57 mg Co/kg; measured value = 0.54 ± 0.01 mg·Co/kg) was included in duplicate with each analysis. Contents of 20 different trace elements and metalloids were determined, among which those of major concern in foods [32–34] included Mn, Ni, Pb, Zn, Co, As, U, Cd, and Cu. Metals and metalloids released by the digestion were added to NH4I solution, extracted by MIBK-TBP (80 : 20), and then stripped with H2O2 (5%), HNO3 (0.5%), and NH4H2PO4 (0.1%). Quantification was done by injecting aliquots of sample solutions (10 μL) into a carbon rod atomizer of an atomic absorption spectrophotometer with a variable detector set at 0.5 absorbance unit full scale and the results expressed in mg/kg of dry matter of each crop species. 2.2.2. Collection and Analysis of Water Samples For water samples, every effort was made to maintain a high degree of cleanliness for all equipment including bottles, containers, and rope and filtering equipment. At each location, water samples were collected in areas near mining activities or metallurgical factories (n = 43), but also in areas far from mining or mineral processing sites (n = 23) from rivers (n = 13), domestic wells or boreholes (n = 43) and taps (n = 23) in the districts of Chingola (n = 21), Kitwe (n = 11), and Luanshya (n = 10) in Zambia and in the cities of Lubumbashi (n = 6) and Likasi (n = 19), and the Kipushi Territory (n = 9) in the DRC always between 8 and 11 h. There were 205 samples collected in the fringe areas of mining activities and 75 control samples from areas far from mining and metallurgical industries. For surface rivers, the sampling was always at midstream or in the main flow and away from slumping and scouring effects found near the banks. The sampling bottle was uncapped immediately before sampling and plunged into the river with the opening facing upstream into the current until it was filled. Then, it was lifted out of water, decanted for a small amount if required, and recapped immediately ensuring hands did not come into contact with the insides of the bottles or caps. Adequate water quantities were obtained from a full flow out of faucets/taps after taps or pumps were left to run for at least two minutes to clear the line (Figure 2). Water was slowly filled in 40 mL clean polystyrene bottles with leak-proof screw caps (Plastiques Gosselin, Hazebrouck, France) to below the container rim before tightening the lids securely. In the deep dug boreholes or wells, water was obtained using tins cut on one side or plastic containers connected to long wooden canes with wire or rope (Figure 2) and filled in the polystyrene bottles. Samples were then pipetted into 1.5 mL Eppendorf tubes using micropipettes and transported in cooler boxes to the laboratory to be stored in the refrigerator at −20°C to retard potential chemical and biological changes before shipping in sealed cooler boxes with ice packs for analysis. Collected samples were filtered (0.45 μm) and measured by ICP-OES. The NIST certified water was included (certified value = 27 μg Co/L, measured value = 26 ± 1 μg·Co/L). Prior to analysis, water samples were filtered using a μm micropore membrane filter (0.45 μm) to avoid clogging the atomizer burner and then trace metal contents were quantified following the description by Muimba-Kankolongo et al. [31]. In particular, they were analyzed using inductively coupled argon plasma mass spectrometry (ICP-MS) with the lowest detection limit of 0.5 ppb (Perkin-Elmer Optima 3300 DV, Norwalk, CT, USA). The NIST-certified water was included (certified value = 27 μg Co/L, measured value = 26 ± 1 μg Co/L). Detection limits for all samples are calculated as twice the standard deviation of 6 preparation blank sample measurements as described by Cheyns et al. [39]. For values below the detection limits, half of the detection limit of each trace element was considered and the results were expressed in μg/L of water. 2.2.3. Collection and Analysis of Urine Samples Urine samples were obtained only from the DRC and not in Zambia because of some administrative issues with the Ministry of Health. Donors of urine samples included females and males among them there were children and adults. The youngest was 2 years old, while the oldest was 58 years old. The collection was from community members composed of infants and children over 2 years old (n = 9), adolescents (n = 4), adults (n = 13), and the elderly (n = 3) in Kabesha and Kawama locations in Lubumbashi following procedures previously described by Banza Lubaba et al. [37]. The collection was during the whole day often with assistance from local health personnel, and participants—both parents and children—were duly informed of the need for urine in the study before samples were collected and their participation was purely based on their willingness. During collection, instructions were provided to participants on how to perform a proper collection to avoid external contamination of the urine. After collection, an aliquot of 5 N hydrochloric acid was added to prevent decomposition and loss of metals by precipitation and then immediately stored in a cooler box and taken to the laboratory for storage in a refrigerator until transportation to Belgium for analysis, using commercial flights. Only conta +raw_completion_output: |- + location: Lubumbashi;Likasi;Kipushi Territory in Haut-Katanga Province;Chingola;Kitwe;Luanshya Districts;Kabecha;Tshansansa;Kasongo;SNCC-Shituru;Gécamines-Shituru;Panda cities;Kansalabwe village;Mungoshi;Douane areas;Betty City;Kampemba farm;Nkumanwa village;Shimulala;Heleni-Kasenji;Kalipenta;Pule;Chama villages;Roan area;Mpatamatu;Mwansa villages;Chankalamu village;Wusakile;Nkana West compounds + environmental_material: water;food crops;ambient air;soil + environments: mining area;metallurgic industry area;farmland;domestic wells;boreholes;rivers + causal_relationships: effect of trace metals on population health;effect of hazardous chemicals on health;effect of long-term exposure to hazardous chemicals on health + variables: trace metals;population health;chemical exposure;food crops;ambient air;soil particles;debris;trace elements;metalloids;Mn;Ni;Pb;Zn;Co;As;U;Cd;Cu + measurements: b5 μg·Co/L;0.57 mg Co/kg (certified value);0.54 ± 0.01 mg·Co/kg (measured value);certified value = 27 μg Co/L;measured value = 26 ± 1 μg·Co/L;values below detection limits;half of the detection limit of each trace element;results expressed in mg/kg of dry matter of each crop species;results expressed in μg/L of water +prompt: |+ + Split the following piece of text into fields in the following format: + + value: <the value of the measurement> + unit: <the unit of the measurement> + + + Text: + results expressed in μg/L of water + + === + +extracted_object: + location: + - Lubumbashi + - Likasi + - GAZ:00031641 + - Chingola + - GAZ:00052656 + - GAZ:00015146 + - Kabecha + - Tshansansa + - Kasongo + - SNCC-Shituru + - Gécamines-Shituru + - GAZ:00239264 + - Kansalabwe village + - Mungoshi + - ENVTHES:21533 + - Betty City + - GAZ:00235468 + - Nkumanwa village + - Shimulala + - Heleni-Kasenji + - Kalipenta + - Pule + - Chama villages + - ENVTHES:21533 + - Mpatamatu + - Mwansa villages + - Chankalamu village + - Wusakile + - Nkana West compounds + environmental_material: + - ENVO:00002006 + - ENVTHES:20523 + - ENVTHES:23 + - ENVO:00001998 + environments: + - ENVTHES:21533 + - ENVTHES:21533 + - farmland + - domestic wells + - ENVO:00002226 + - ENVO:00000022 + causal_relationships: + - cause: ENVO:01001069 + effect: ENVTHES:20715 + - cause: ENVTHES:21964 + effect: health + - cause: ENVTHES:21964 + effect: health + variables: + - ENVO:01001069 + - ENVTHES:20715 + - ENVTHES:21964 + - ENVTHES:20523 + - ENVO:00002005 + - ENVO:00001998 + - debris + - trace elements + - metalloids + - Mn + - Ni + - Pb + - Zn + - Co + - As + - U + - Cd + - Cu + measurements: + - value: b5 + unit: μg·Co/L + - value: 0.54 ± 0.01 + unit: mg·Co/kg + - value: '27' + unit: μg Co/L + - value: 26 ± 1 + unit: μg·Co/L + - value: values below detection limits + unit: None + - value: each + unit: trace element + - value: unknown + unit: mg/kg of dry matter + - value: results + unit: μg/L +named_entities: + - id: GAZ:00031641 + label: Kipushi Territory in Haut-Katanga Province + - id: GAZ:00052656 + label: Kitwe + - id: GAZ:00015146 + label: Luanshya Districts + - id: GAZ:00239264 + label: Panda cities + - id: GAZ:00235468 + label: Kampemba farm + - id: ENVO:00002226 + label: boreholes + - id: ENVO:00000022 + label: rivers + - id: ENVO:01001069 + label: trace metals + - id: ENVTHES:21964 + label: hazardous chemicals diff --git a/notebooks/text.txt b/notebooks/text.txt new file mode 100644 index 000000000..00c76bf82 --- /dev/null +++ b/notebooks/text.txt @@ -0,0 +1 @@ +Spain is a significant contributor to the global agricultural sector, with its primary exports demonstrating the country's diverse climate and agricultural capacity. The nation leads the world in olive oil production and export, renowned for its quality. Spain is also one of the top wine producers globally, with notable regions including Rioja and Ribera del Duero. It exports a wide range of fruits, particularly citrus fruits such as oranges and lemons from Valencia, as well as peaches, strawberries, melons, and apples. Vegetable exports are substantial, with tomatoes, peppers, cucumbers, and lettuce being predominant, especially from the Almería region known for its greenhouse production. Spain is recognized for its premium pork products, notably jamón ibérico and jamón serrano, and is a leading exporter of nuts, particularly almonds and hazelnuts. Additionally, Spain exports significant quantities of fish and seafood, including sardines, tuna, and shrimp, facilitated by its extensive coastline and fishing traditions. \ No newline at end of file diff --git a/notebooks/text2.txt b/notebooks/text2.txt new file mode 100644 index 000000000..552afcda2 --- /dev/null +++ b/notebooks/text2.txt @@ -0,0 +1 @@ +Zambia and the DR Congo are situated in the central African Copperbelt, which is part of the Lufilian geological structure arc stretching over from Kolwezi in Katanga Province in the DRC to Luanshya in Copperbelt Province in Zambia. The area has large copper-cobalt deposits of which the extraction causes severe ecosystem damage due to pollution of water, food crops, and the ambient air negatively impacting population health. Contamination of drinking water for domestic use and foods (cereals, roots and tubers, vegetables, and fruits) was determined by assessing the contents of trace metals including Mn, Ni, Pb, Zn, Co, As, U, Cd, and Cu and through a questionnaire for environmental damage. Food samples were analyzed by inductively coupled argon plasma/optical emission spectroscopy (ICP-OES), while water and urine samples were analyzed by inductively coupled argon plasma mass spectrometry (ICP-MS). Concentrations of Ni, Pb, and Cd were higher in almost all food crops, although Cu was more in samples of Cucurbita maxima and Amaranthus hybridus. Mean contents (μg/L) of Mn, Zn, Cd, Pb, and U were, respectively, 5,454.6, 2552.2, 138.7, 39.7, 2361.1, and 21.4 in the DRC and 108.9, 543.3, 0.3, 0.2, 1.5, and 0.5 in Zambia, being significantly higher and always far above World Health Organization maximum limits in the DRC. Urine samples taken only from the DRC contained trace metals with children's samples being more contaminated than adult ones. Our results conclusively echo the most critical challenges of toxic pollutants causing numerous health issues among the population. Given an outcry among households adjacent to mines about land degradation and food spoilage, and health problems over years, joint efforts are needed from public and private sectors for stringent mining exploitation monitoring for sustainable governance to protect the environment and ensure food and nutrition safety, and population well-being in Zambia and the DR Congo. \ No newline at end of file From 00be7ca0690e88179f52f504a46f90698af95f1e Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 13:43:37 -0400 Subject: [PATCH 28/40] Verify quick examples notebook works --- notebooks/Quick-Examples.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/notebooks/Quick-Examples.ipynb b/notebooks/Quick-Examples.ipynb index 9a6cc41d7..2f2d78a23 100644 --- a/notebooks/Quick-Examples.ipynb +++ b/notebooks/Quick-Examples.ipynb @@ -11,7 +11,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Last updated May 28, 2024" + "Last updated Jul 19, 2024" ] }, { From 4ba90ba4ea189854bcbf391fa7fe29e035bcfcfd Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 13:44:11 -0400 Subject: [PATCH 29/40] Linting --- src/ontogpt/converters/ontology_converter.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/ontogpt/converters/ontology_converter.py b/src/ontogpt/converters/ontology_converter.py index 5efc4287c..3962867cc 100644 --- a/src/ontogpt/converters/ontology_converter.py +++ b/src/ontogpt/converters/ontology_converter.py @@ -1,4 +1,5 @@ """Ontology converter.""" + import logging from dataclasses import dataclass, field from pathlib import Path From 865deb1a0fd80404ab7196717306b0e3576b0d1a Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 13:44:55 -0400 Subject: [PATCH 30/40] Remove re from imports --- src/ontogpt/cli.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/ontogpt/cli.py b/src/ontogpt/cli.py index 4a3dbe8b5..574c659d9 100644 --- a/src/ontogpt/cli.py +++ b/src/ontogpt/cli.py @@ -4,7 +4,6 @@ import json import logging import pickle -import re import sys from copy import deepcopy from dataclasses import dataclass From 5ab184d516b8813addd1a47f28ccfd1c51ea8dc6 Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 13:47:05 -0400 Subject: [PATCH 31/40] Linting and cleanup --- src/ontogpt/utils/output_parser.py | 52 +++++++++---- src/ontogpt/utils/output_parser_bulleted.py | 82 ++++++++++++++++----- 2 files changed, 102 insertions(+), 32 deletions(-) diff --git a/src/ontogpt/utils/output_parser.py b/src/ontogpt/utils/output_parser.py index 0dfd26ba0..c15e2bd88 100644 --- a/src/ontogpt/utils/output_parser.py +++ b/src/ontogpt/utils/output_parser.py @@ -1,14 +1,26 @@ -import yaml +"""Parser utilities for handling output.""" + import time -import pprint from oaklib import get_adapter -NULL_VALS = ['', 'Not mentioned', 'none mentioned', 'Not mentioned in the text', - 'Not mentioned in the provided text.', 'No exposures mentioned in the text.', - 'None', 'N/A', 'No exposures mentioned in the text.', 'None mentioned in the text', - 'Not mentioned in the text.', 'None relevant', 'None mentioned in the text.', - 'No gene to molecular activity relationships mentioned in the text.', - 'No genes mentioned', 'No genes mentioned in the text.'] +NULL_VALS = [ + "", + "Not mentioned", + "none mentioned", + "Not mentioned in the text", + "Not mentioned in the provided text.", + "No exposures mentioned in the text.", + "None", + "N/A", + "No exposures mentioned in the text.", + "None mentioned in the text", + "Not mentioned in the text.", + "None relevant", + "None mentioned in the text.", + "No gene to molecular activity relationships mentioned in the text.", + "No genes mentioned", + "No genes mentioned in the text.", +] lines = [] # adapter = get_adapter("sqlite:obo:CHEBI") adapter = get_adapter("sqlite:obo:MONDO") @@ -17,6 +29,7 @@ # output_file = "output_100_0818.yaml" output_file = "output_partial_50_0911.yaml" + def tripleprint(dict): key = next(iter(dict)) for i in range(len(dict[key])): @@ -24,20 +37,29 @@ def tripleprint(dict): for value in dict.values(): curr.append(value[i]) print(curr) + + def forprint(lst): for elem in lst: print(elem) + + def nprint(lst, n): for i in range(n): print(lst[i]) + + def sleepprint(lst): for elem in lst: print(elem) time.sleep(0.5) + + def enumprint(lst): for index, elem in enumerate(lst): print(str(index + 1) + ":\t" + str(elem)) + with open(output_file, "r") as file: to_print = False perpetuators = tuple([" subject:", " predicate:", " object:", " "]) @@ -45,20 +67,20 @@ def enumprint(lst): for line in file: line = line.strip("\n") if line.startswith("extracted_object:"): - # if line.startswith(" disease_cellular_process_relationships:") and not line.startswith(" disease_cellular_process_relationships: "): + # if line.startswith(" disease_cellular_process_relationships:") and not line.startswith(" disease_cellular_process_relationships: "): to_print = True elif not line.startswith(perpetuators): to_print = False if to_print: lines.append(line) -cleaned_lines = [x for x in list(filter(lambda elem: not(elem.isspace()), lines)) if x.strip()] +cleaned_lines = [x for x in list(filter(lambda elem: not (elem.isspace()), lines)) if x.strip()] cleaned_lines = [x for x in cleaned_lines if x != "extracted_object: {}"] i = 1 while i < len(cleaned_lines): if cleaned_lines[i].startswith(" "): - cleaned_lines[i-1] += " " - cleaned_lines[i-1] += cleaned_lines[i][4:] + cleaned_lines[i - 1] += " " + cleaned_lines[i - 1] += cleaned_lines[i][4:] del cleaned_lines[i] else: i += 1 @@ -68,14 +90,14 @@ def enumprint(lst): i = 0 while i < len(cleaned_lines): if cleaned_lines[i].startswith(header): - for index, elem in enumerate(cleaned_lines[i+1:i+4]): + for index, elem in enumerate(cleaned_lines[i + 1 : i + 4]): if elem.startswith(header): next_index = i + 1 + index del cleaned_lines[i:next_index] i -= 1 i += 1 -grouped_lines = [cleaned_lines[n:n+4] for n in range(0, len(cleaned_lines), 4)] +grouped_lines = [cleaned_lines[n : n + 4] for n in range(0, len(cleaned_lines), 4)] # trimmed_dict = {"genes": [], "relationships": [], "exposures": []} trimmed_dict = {"diseases": [], "relationships": [], "cellular processes": []} @@ -124,4 +146,4 @@ def enumprint(lst): curr[0] = adapter.label(curr[0]) subjects_with_names.append(curr) -# forprint(subjects_with_names) \ No newline at end of file +# forprint(subjects_with_names) diff --git a/src/ontogpt/utils/output_parser_bulleted.py b/src/ontogpt/utils/output_parser_bulleted.py index 5d7c3d057..3c8697e33 100644 --- a/src/ontogpt/utils/output_parser_bulleted.py +++ b/src/ontogpt/utils/output_parser_bulleted.py @@ -1,14 +1,26 @@ -import yaml +"""Output parser utilities for bulleted output.""" + import time -import pprint from oaklib import get_adapter -NULL_VALS = ['', 'Not mentioned', 'none mentioned', 'Not mentioned in the text', - 'Not mentioned in the provided text.', 'No exposures mentioned in the text.', - 'None', 'N/A', 'No exposures mentioned in the text.', 'None mentioned in the text', - 'Not mentioned in the text.', 'None relevant', 'None mentioned in the text.', - 'No gene to molecular activity relationships mentioned in the text.', - 'No genes mentioned', 'No genes mentioned in the text.'] +NULL_VALS = [ + "", + "Not mentioned", + "none mentioned", + "Not mentioned in the text", + "Not mentioned in the provided text.", + "No exposures mentioned in the text.", + "None", + "N/A", + "No exposures mentioned in the text.", + "None mentioned in the text", + "Not mentioned in the text.", + "None relevant", + "None mentioned in the text.", + "No gene to molecular activity relationships mentioned in the text.", + "No genes mentioned", + "No genes mentioned in the text.", +] lines = [] adapter = get_adapter("sqlite:obo:MONDO") # output_file = "output_2000_0719.yaml" @@ -16,6 +28,7 @@ # output_file = "output_100_0818.yaml" output_file = "output_100.0911.yaml" + def tripleprint(dict): key = next(iter(dict)) for i in range(len(dict[key])): @@ -23,34 +36,56 @@ def tripleprint(dict): for value in dict.values(): curr.append(value[i]) print(curr) + + def forprint(lst): for elem in lst: print(elem) + + def forprint_newline(lst): for elem in lst: print(elem) print("\n") + + def nprint(lst, n): for i in range(n): print(lst[i]) + + def sleepprint(lst): for elem in lst: print(elem) time.sleep(0.5) + + def enumprint(lst): for index, elem in enumerate(lst): print(str(index + 1) + ":\t" + str(elem)) + with open(output_file, "r") as file: to_print = False # perpetuators = tuple([" subject:", " predicate:", " object:", " "]) perpetuators = tuple([" - subject:", " predicate:", " object:"]) - perpetuators = tuple([" - subject:", " predicate:", " object:", " qualifier:", " subject_qualifier:", " object_qualifier:"]) + perpetuators = tuple( + [ + " - subject:", + " predicate:", + " object:", + " qualifier:", + " subject_qualifier:", + " object_qualifier:", + ] + ) for line in file: line = line.strip("\n") # if line.startswith("extracted_object:"): - if line.startswith(" disease_cellular_process_relationships:") and not line.startswith(" disease_cellular_process_relationships: "): - # if line.startswith(perpetuators): + if line.startswith(" disease_cellular_process_relationships:") and not line.startswith( + " disease_cellular_process_relationships: " + ): + # if line.startswith(perpetuators): to_print = True # elif not line.startswith(perpetuators): # if line.startswith("named_entities:"): @@ -59,14 +94,27 @@ def enumprint(lst): if to_print: lines.append(line) -cleaned_lines = [x for x in list(filter(lambda elem: not(elem.isspace()), lines)) if x.strip()] -cleaned_lines = [x for x in cleaned_lines if not x.startswith(tuple([" qualifier:", " subject_qualifier:", " object_qualifier:", " disease_cellular_process_relationships:"]))] +cleaned_lines = [x for x in list(filter(lambda elem: not (elem.isspace()), lines)) if x.strip()] +cleaned_lines = [ + x + for x in cleaned_lines + if not x.startswith( + tuple( + [ + " qualifier:", + " subject_qualifier:", + " object_qualifier:", + " disease_cellular_process_relationships:", + ] + ) + ) +] header = " - subject:" i = 0 while i < len(cleaned_lines): if cleaned_lines[i].startswith(header): - for index, elem in enumerate(cleaned_lines[i+1:i+3]): + for index, elem in enumerate(cleaned_lines[i + 1 : i + 3]): if elem.startswith(header): next_index = i + 1 + index del cleaned_lines[i:next_index] @@ -75,11 +123,11 @@ def enumprint(lst): cleaned_lines = [x.strip() for x in cleaned_lines] for i, line in enumerate(cleaned_lines.copy()): -# for line in cleaned_lines: + # for line in cleaned_lines: if line.startswith("- "): cleaned_lines[i] = line[2:] -grouped_lines = [cleaned_lines[n:n+3] for n in range(0, len(cleaned_lines), 3)] +grouped_lines = [cleaned_lines[n : n + 3] for n in range(0, len(cleaned_lines), 3)] trimmed_dict = {"diseases": [], "relationships": [], "cellular processes": []} for group in grouped_lines: subject = group[0].split(":", 1)[1].strip() @@ -122,4 +170,4 @@ def enumprint(lst): curr[0] = adapter.label(curr[0]) subjects_with_names.append(curr) -# forprint(subjects_with_names) \ No newline at end of file +# forprint(subjects_with_names) From 2144f76d1803a486ab8fb3b35e72c768fbd84102 Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 13:49:35 -0400 Subject: [PATCH 32/40] More linting --- src/ontogpt/utils/output_parser.py | 5 +++-- src/ontogpt/utils/output_parser_bulleted.py | 2 +- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/src/ontogpt/utils/output_parser.py b/src/ontogpt/utils/output_parser.py index c15e2bd88..51913eae0 100644 --- a/src/ontogpt/utils/output_parser.py +++ b/src/ontogpt/utils/output_parser.py @@ -67,7 +67,8 @@ def enumprint(lst): for line in file: line = line.strip("\n") if line.startswith("extracted_object:"): - # if line.startswith(" disease_cellular_process_relationships:") and not line.startswith(" disease_cellular_process_relationships: "): + # if line.startswith(" disease_cellular_process_relationships:") + # and not line.startswith(" disease_cellular_process_relationships: "): to_print = True elif not line.startswith(perpetuators): to_print = False @@ -118,7 +119,7 @@ def enumprint(lst): for key, value in trimmed_dict.copy().items(): for i, elem in enumerate(value): if elem.lower() in (val.lower() for val in NULL_VALS): - for key, value in trimmed_dict.items(): + for _key, value in trimmed_dict.items(): del value[i] # subjects_with_chebi = [] diff --git a/src/ontogpt/utils/output_parser_bulleted.py b/src/ontogpt/utils/output_parser_bulleted.py index 3c8697e33..50bda0d33 100644 --- a/src/ontogpt/utils/output_parser_bulleted.py +++ b/src/ontogpt/utils/output_parser_bulleted.py @@ -140,7 +140,7 @@ def enumprint(lst): for key, value in trimmed_dict.copy().items(): for i, elem in enumerate(value): if elem.lower() in (val.lower() for val in NULL_VALS): - for key, value in trimmed_dict.items(): + for _key, value in trimmed_dict.items(): del value[i] # subjects_with_chebi = [] From bbdc1d01480fb58d69cf85c11061dd11d6115366 Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 15:56:44 -0400 Subject: [PATCH 33/40] Clean up yaml wrapper --- src/ontogpt/io/yaml_wrapper.py | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/src/ontogpt/io/yaml_wrapper.py b/src/ontogpt/io/yaml_wrapper.py index 4a3c4aadf..682671a36 100644 --- a/src/ontogpt/io/yaml_wrapper.py +++ b/src/ontogpt/io/yaml_wrapper.py @@ -1,4 +1,5 @@ """YAML Wrapper.""" + import io import logging from typing import Any, Optional, TextIO @@ -6,9 +7,6 @@ import pydantic from ruamel.yaml import YAML, RoundTripRepresenter -# import yaml -# from yaml import SafeDumper - logger = logging.getLogger(__name__) @@ -28,11 +26,6 @@ def eliminate_empty(obj: Any, preserve=False) -> Any: return obj -# SafeDumper.add_representer(str, -# lambda dumper, value: dumper.represent_scalar('tag:yaml.org,2002:str', value, style='|') -# ) - - def repr_str(dumper: RoundTripRepresenter, data: str): if "\n" in data: return dumper.represent_scalar("tag:yaml.org,2002:str", data, style="|") @@ -40,7 +33,7 @@ def repr_str(dumper: RoundTripRepresenter, data: str): def dump_minimal_yaml(obj: Any, minimize=True, file: Optional[TextIO] = None) -> str: - """Dump a YAML string, but eliminating Nones and empty lists and dicts.""" + """Dump a YAML string, but eliminate Nones and empty lists and dicts.""" yaml = YAML() yaml.representer.add_representer(str, repr_str) yaml.default_flow_style = False From d20105b74144a3586dcff038aafab38ec8a4fc4c Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 15:58:13 -0400 Subject: [PATCH 34/40] Linting and updates for IO functions --- src/ontogpt/io/markdown_exporter.py | 3 ++- src/ontogpt/io/rdf_exporter.py | 1 + src/ontogpt/io/template_loader.py | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/src/ontogpt/io/markdown_exporter.py b/src/ontogpt/io/markdown_exporter.py index 55a217001..bc32251b1 100644 --- a/src/ontogpt/io/markdown_exporter.py +++ b/src/ontogpt/io/markdown_exporter.py @@ -1,4 +1,5 @@ """Markdown exporter.""" + from dataclasses import dataclass from io import BytesIO, StringIO, TextIOWrapper from pathlib import Path @@ -47,7 +48,7 @@ def export_object( output: TextIO, indent: int, ): - for field in obj.__fields__.values(): + for field in obj.model_fields.values(): if indent < 0: output.write(f"\n\n### {field.name}\n\n") else: diff --git a/src/ontogpt/io/rdf_exporter.py b/src/ontogpt/io/rdf_exporter.py index e7c0f4c9c..8f0b92b5b 100644 --- a/src/ontogpt/io/rdf_exporter.py +++ b/src/ontogpt/io/rdf_exporter.py @@ -1,4 +1,5 @@ """RDF convertor.""" + import logging from dataclasses import dataclass from io import BytesIO diff --git a/src/ontogpt/io/template_loader.py b/src/ontogpt/io/template_loader.py index 50fbe543d..d1a04811e 100644 --- a/src/ontogpt/io/template_loader.py +++ b/src/ontogpt/io/template_loader.py @@ -34,7 +34,7 @@ def get_template_details(template: TEMPLATE_NAME) -> ClassDefinition: # Check if file exists first if not path_to_template.exists(): raise FileNotFoundError(f"Template file not found at {template}") - + # Copy the schema to the templates directory # So it will have access to imports like the core schema templates_path = this_path.parent / "templates" @@ -47,7 +47,7 @@ def get_template_details(template: TEMPLATE_NAME) -> ClassDefinition: gen = PydanticGenerator(str(new_path_to_template), pydantic_version=2) path_to_module.write_text(gen.serialize()) - + mod = importlib.import_module(f"ontogpt.templates.{module_name}") class_name = None From cc9856248fe7e2eb4715e17a51a10154bca89ab5 Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 15:59:27 -0400 Subject: [PATCH 35/40] Update and format generic exporter class --- src/ontogpt/io/exporter.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/ontogpt/io/exporter.py b/src/ontogpt/io/exporter.py index 36b79b437..b0f87d032 100644 --- a/src/ontogpt/io/exporter.py +++ b/src/ontogpt/io/exporter.py @@ -1,4 +1,5 @@ -"""Exporter.""" +"""Generic exporter class.""" + from dataclasses import dataclass from io import BytesIO from pathlib import Path From 92d2640a87e3a673140c603824df146e73a61b4d Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 16:14:22 -0400 Subject: [PATCH 36/40] GPTReasonMethodType -> LLMReasonMethodType --- src/ontogpt/cli.py | 2 +- src/ontogpt/engines/reasoner_engine.py | 8 ++++---- src/ontogpt/ontex/extractor.py | 23 ++++++++++++----------- 3 files changed, 17 insertions(+), 16 deletions(-) diff --git a/src/ontogpt/cli.py b/src/ontogpt/cli.py index 574c659d9..25bf15357 100644 --- a/src/ontogpt/cli.py +++ b/src/ontogpt/cli.py @@ -1248,7 +1248,7 @@ def reason( tasks = [] print(f"Cloning {len(tc.tasks)} tasks") for core_task in tc.tasks: - for m in extractor.GPTReasonMethodType: + for m in extractor.LLMReasonMethodType: print(f"Cloning {m}") task = deepcopy(core_task) task.method = m diff --git a/src/ontogpt/engines/reasoner_engine.py b/src/ontogpt/engines/reasoner_engine.py index 6c7ae50f1..9377256ac 100644 --- a/src/ontogpt/engines/reasoner_engine.py +++ b/src/ontogpt/engines/reasoner_engine.py @@ -13,7 +13,7 @@ Answer, Axiom, Explanation, - GPTReasonMethodType, + LLMReasonMethodType, Task, TaskCollection, ) @@ -41,7 +41,7 @@ class ReasonerResult(BaseModel): task_name: Optional[str] = None task_type: Optional[str] = None task_obfuscated: Optional[bool] = None - method: Optional[GPTReasonMethodType] = None + method: Optional[LLMReasonMethodType] = None model: Optional[str] = None description: Optional[str] = None answers: Optional[List[Answer]] = None @@ -159,9 +159,9 @@ def reason( examples=task.examples, ) completion_length = self.completion_length - if task.method == GPTReasonMethodType.EXPLANATION: + if task.method == LLMReasonMethodType.EXPLANATION: completion_length *= 2 - elif task.method == GPTReasonMethodType.CHAIN_OF_THOUGHT: + elif task.method == LLMReasonMethodType.CHAIN_OF_THOUGHT: completion_length *= 2 logger.info(f"Prompt: {prompt}") if self.encoding is not None: diff --git a/src/ontogpt/ontex/extractor.py b/src/ontogpt/ontex/extractor.py index e2c514e4d..eb5644865 100644 --- a/src/ontogpt/ontex/extractor.py +++ b/src/ontogpt/ontex/extractor.py @@ -1,4 +1,5 @@ """Tools to extract sub-ontologies and reasoner tasks.""" + import base64 import logging import random @@ -170,7 +171,7 @@ class Example(BaseModel): query_answers: Optional[List[ExampleQueryAnswers]] = None -class GPTReasonMethodType(str, Enum): +class LLMReasonMethodType(str, Enum): BASIC = "basic" EXPLANATION = "explanation" CHAIN_OF_THOUGHT = "chain_of_thought" @@ -198,7 +199,7 @@ class Task(BaseModel): examples: Optional[List[Example]] = None obfuscated: Optional[bool] = False - method: Optional[GPTReasonMethodType] = None + method: Optional[LLMReasonMethodType] = None include_explanations: Optional[bool] = False """If true then completing the task must involve providing explanations for each answer.""" @@ -245,19 +246,19 @@ def populate(self) -> None: def init_method(self): if self.method: logger.info(f"Initializing method for {self.name}") - if not isinstance(self.method, GPTReasonMethodType): - self.method = GPTReasonMethodType(self.method) - if self.method == GPTReasonMethodType.EXPLANATION: + if not isinstance(self.method, LLMReasonMethodType): + self.method = LLMReasonMethodType(self.method) + if self.method == LLMReasonMethodType.EXPLANATION: self.include_explanations = True - elif self.method == GPTReasonMethodType.CHAIN_OF_THOUGHT: + elif self.method == LLMReasonMethodType.CHAIN_OF_THOUGHT: self.chain_of_thought = True else: if self.include_explanations: - self.method = GPTReasonMethodType.EXPLANATION + self.method = LLMReasonMethodType.EXPLANATION elif self.chain_of_thought: - self.method = GPTReasonMethodType.CHAIN_OF_THOUGHT + self.method = LLMReasonMethodType.CHAIN_OF_THOUGHT else: - self.method = GPTReasonMethodType.BASIC + self.method = LLMReasonMethodType.BASIC class OntologyCoherencyTask(Task): @@ -1050,9 +1051,9 @@ def load(file_or_object: Union[dict, str, Path, TextIO]): typ = task_dict["type"] cls = current_module.__dict__[typ] task = cls(**task_dict) - if not isinstance(task.method, GPTReasonMethodType): + if not isinstance(task.method, LLMReasonMethodType): # TODO: figure how to get pydantic to do this - task.method = GPTReasonMethodType(task.method) + task.method = LLMReasonMethodType(task.method) tasks.append(task) tc_dict["tasks"] = tasks return TaskCollection(**tc_dict) From 693002ffc106ec3daefb647fcf0faa8d08792da2 Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 16:17:04 -0400 Subject: [PATCH 37/40] Linting --- src/ontogpt/utils/output_parser.py | 2 +- src/ontogpt/utils/output_parser_bulleted.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontogpt/utils/output_parser.py b/src/ontogpt/utils/output_parser.py index 51913eae0..113ecb3f8 100644 --- a/src/ontogpt/utils/output_parser.py +++ b/src/ontogpt/utils/output_parser.py @@ -116,7 +116,7 @@ def enumprint(lst): trimmed_dict["relationships"].append(relation) trimmed_dict["cellular processes"].append(object) -for key, value in trimmed_dict.copy().items(): +for _key, value in trimmed_dict.copy().items(): for i, elem in enumerate(value): if elem.lower() in (val.lower() for val in NULL_VALS): for _key, value in trimmed_dict.items(): diff --git a/src/ontogpt/utils/output_parser_bulleted.py b/src/ontogpt/utils/output_parser_bulleted.py index 50bda0d33..8de905635 100644 --- a/src/ontogpt/utils/output_parser_bulleted.py +++ b/src/ontogpt/utils/output_parser_bulleted.py @@ -137,7 +137,7 @@ def enumprint(lst): trimmed_dict["relationships"].append(relation) trimmed_dict["cellular processes"].append(object) -for key, value in trimmed_dict.copy().items(): +for _key, value in trimmed_dict.copy().items(): for i, elem in enumerate(value): if elem.lower() in (val.lower() for val in NULL_VALS): for _key, value in trimmed_dict.items(): From a63c716b4156bf5a57ae1a50acbb7113ca518d8a Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 16:29:47 -0400 Subject: [PATCH 38/40] Type fixes --- src/ontogpt/utils/output_parser.py | 4 ++-- src/ontogpt/utils/output_parser_bulleted.py | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/ontogpt/utils/output_parser.py b/src/ontogpt/utils/output_parser.py index 113ecb3f8..6a8596632 100644 --- a/src/ontogpt/utils/output_parser.py +++ b/src/ontogpt/utils/output_parser.py @@ -101,7 +101,7 @@ def enumprint(lst): grouped_lines = [cleaned_lines[n : n + 4] for n in range(0, len(cleaned_lines), 4)] # trimmed_dict = {"genes": [], "relationships": [], "exposures": []} -trimmed_dict = {"diseases": [], "relationships": [], "cellular processes": []} +trimmed_dict: dict = {"diseases": [], "relationships": [], "cellular processes": []} for group in grouped_lines: group.pop(0) @@ -143,7 +143,7 @@ def enumprint(lst): subjects_with_names = [] # for elem in subjects_with_chebi: for elem in subjects_with_mondo: - curr = elem[:] + curr = [elem[:]] curr[0] = adapter.label(curr[0]) subjects_with_names.append(curr) diff --git a/src/ontogpt/utils/output_parser_bulleted.py b/src/ontogpt/utils/output_parser_bulleted.py index 8de905635..b5bc84ad1 100644 --- a/src/ontogpt/utils/output_parser_bulleted.py +++ b/src/ontogpt/utils/output_parser_bulleted.py @@ -128,7 +128,7 @@ def enumprint(lst): cleaned_lines[i] = line[2:] grouped_lines = [cleaned_lines[n : n + 3] for n in range(0, len(cleaned_lines), 3)] -trimmed_dict = {"diseases": [], "relationships": [], "cellular processes": []} +trimmed_dict: dict = {"diseases": [], "relationships": [], "cellular processes": []} for group in grouped_lines: subject = group[0].split(":", 1)[1].strip() relation = group[1].split(":", 1)[1].strip() @@ -145,7 +145,7 @@ def enumprint(lst): # subjects_with_chebi = [] # objects_with_ecto = [] -subjects_with_mondo = [] +subjects_with_mondo: list = [] mondo_go = [] key = next(iter(trimmed_dict)) for i in range(len(trimmed_dict[key])): @@ -166,7 +166,7 @@ def enumprint(lst): subjects_with_names = [] # for elem in subjects_with_chebi: for elem in subjects_with_mondo: - curr = elem[:] + curr = [elem[:]] curr[0] = adapter.label(curr[0]) subjects_with_names.append(curr) From 6d0342badf0789367a51bcbcef5f3bf110a476b4 Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 16:34:13 -0400 Subject: [PATCH 39/40] Type fixes and comments --- src/ontogpt/utils/output_parser.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/ontogpt/utils/output_parser.py b/src/ontogpt/utils/output_parser.py index 6a8596632..9f0694954 100644 --- a/src/ontogpt/utils/output_parser.py +++ b/src/ontogpt/utils/output_parser.py @@ -3,6 +3,9 @@ import time from oaklib import get_adapter +# TODO: Set this up to be more general +# TODO: merge the null checker into the knowledge engine + NULL_VALS = [ "", "Not mentioned", @@ -143,7 +146,7 @@ def enumprint(lst): subjects_with_names = [] # for elem in subjects_with_chebi: for elem in subjects_with_mondo: - curr = [elem[:]] + curr = [elem] curr[0] = adapter.label(curr[0]) subjects_with_names.append(curr) From 1cb45637235f1c75e5d9ffd88d71787f288a2ce1 Mon Sep 17 00:00:00 2001 From: caufieldjh <j.harry.caufield@gmail.com> Date: Fri, 19 Jul 2024 16:42:28 -0400 Subject: [PATCH 40/40] OK let's just ignore this line --- src/ontogpt/utils/output_parser.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/ontogpt/utils/output_parser.py b/src/ontogpt/utils/output_parser.py index 9f0694954..b1b756249 100644 --- a/src/ontogpt/utils/output_parser.py +++ b/src/ontogpt/utils/output_parser.py @@ -129,6 +129,7 @@ def enumprint(lst): # objects_with_ecto = [] subjects_with_mondo = [] key = next(iter(trimmed_dict)) +curr: list[str] = [] for i in range(len(trimmed_dict[key])): curr = [] for value in trimmed_dict.values(): @@ -145,8 +146,8 @@ def enumprint(lst): subjects_with_names = [] # for elem in subjects_with_chebi: -for elem in subjects_with_mondo: - curr = [elem] +for elem in subjects_with_mondo: # type: ignore + curr.append(elem) curr[0] = adapter.label(curr[0]) subjects_with_names.append(curr)